Starting phenix.real_space_refine on Mon May 4 01:00:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.cif Found real_map, /net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.map" model { file = "/net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11na_75854/05_2026/11na_75854.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 138 5.16 5 C 10168 2.51 5 N 2702 2.21 5 O 3584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16626 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 456} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 185 Classifications: {'water': 185} Link IDs: {None: 184} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 30.263 44.724 59.082 1.00 47.20 S ATOM 1170 SG CYS A 154 35.756 26.518 46.621 1.00 44.12 S ATOM 4552 SG CYS B 95 38.781 30.027 43.702 1.00 33.96 S ATOM 465 SG CYS A 62 36.655 32.931 48.697 1.00 25.91 S ATOM 652 SG CYS A 88 41.572 28.255 49.258 1.00 39.32 S ATOM 652 SG CYS A 88 41.572 28.255 49.258 1.00 39.32 S ATOM 5005 SG CYS B 153 40.023 24.422 44.894 1.00 42.79 S ATOM 4372 SG CYS B 70 45.295 28.938 43.458 1.00 18.84 S ATOM 4552 SG CYS B 95 38.781 30.027 43.702 1.00 33.96 S ATOM 10053 SG CYS C 275 105.727 56.202 59.522 1.00 88.89 S ATOM 9134 SG CYS C 154 100.119 74.678 46.979 1.00 37.73 S ATOM 12513 SG CYS D 95 96.633 71.429 43.785 1.00 32.20 S ATOM 8429 SG CYS C 62 99.194 68.065 49.187 1.00 38.53 S ATOM 8616 SG CYS C 88 94.099 71.773 50.207 1.00 29.93 S ATOM 12966 SG CYS D 153 95.402 76.753 45.239 1.00 35.80 S ATOM 12333 SG CYS D 70 89.875 72.384 43.536 1.00 38.39 S ATOM 12513 SG CYS D 95 96.633 71.429 43.785 1.00 32.20 S Time building chain proxies: 4.79, per 1000 atoms: 0.29 Number of scatterers: 16626 At special positions: 0 Unit cell: (135.975, 102.165, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 138 16.00 O 3584 8.00 N 2702 7.00 C 10168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 867.5 milliseconds 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 58.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.910A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.861A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.775A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.190A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.061A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.559A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 316 removed outlier: 4.136A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 370 removed outlier: 5.616A pdb=" N ILE A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA A 366 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.178A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.621A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.809A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 4.090A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.615A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.982A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.774A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.502A pdb=" N ALA B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.857A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.178A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.617A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.687A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.534A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 19 removed outlier: 4.434A pdb=" N VAL C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.188A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.463A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.652A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.160A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.130A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.547A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 6.110A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.709A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 347 Processing helix chain 'C' and resid 359 through 370 removed outlier: 3.924A pdb=" N ILE C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA C 366 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.342A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.608A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 4.005A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.552A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.691A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.174A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.323A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.901A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.002A pdb=" N THR D 263 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 removed outlier: 3.549A pdb=" N HIS D 297 " --> pdb=" O GLN D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 294 through 297' Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.407A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.467A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.882A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.829A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 252 removed outlier: 8.103A pdb=" N VAL A 223 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 252 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 225 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.583A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.648A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.406A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 5.778A pdb=" N LYS C 349 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL C 375 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR C 377 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 353 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR C 379 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 355 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.323A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 252 removed outlier: 7.674A pdb=" N VAL C 223 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN C 252 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 225 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN C 271 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.318A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.378A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2211 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: 3.02 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 16158 1.55 - 1.90: 185 1.90 - 2.25: 38 2.25 - 2.60: 80 2.60 - 2.95: 18 Bond restraints: 16479 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.953 -0.753 2.00e-02 2.50e+03 1.42e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.920 -0.720 2.00e-02 2.50e+03 1.30e+03 bond pdb="FE4 CLF A 503 " pdb="FE5 CLF A 503 " ideal model delta sigma weight residual 2.200 2.903 -0.703 2.00e-02 2.50e+03 1.24e+03 bond pdb="FE2 CLF A 503 " pdb="FE8 CLF A 503 " ideal model delta sigma weight residual 2.200 2.889 -0.689 2.00e-02 2.50e+03 1.19e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.851 -0.651 2.00e-02 2.50e+03 1.06e+03 ... (remaining 16474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.88: 22222 6.88 - 13.75: 8 13.75 - 20.63: 2 20.63 - 27.50: 0 27.50 - 34.38: 4 Bond angle restraints: 22236 Sorted by residual: angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE4 CLF A 503 " ideal model delta sigma weight residual 90.00 55.62 34.38 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.85 34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.14 32.86 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE1 CLF A 503 " ideal model delta sigma weight residual 90.00 57.15 32.85 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE3 CLF A 503 " ideal model delta sigma weight residual 90.00 107.40 -17.40 3.00e+00 1.11e-01 3.36e+01 ... (remaining 22231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9237 17.94 - 35.88: 684 35.88 - 53.83: 112 53.83 - 71.77: 34 71.77 - 89.71: 29 Dihedral angle restraints: 10096 sinusoidal: 4358 harmonic: 5738 Sorted by residual: dihedral pdb=" CA ASP D 215 " pdb=" CB ASP D 215 " pdb=" CG ASP D 215 " pdb=" OD1 ASP D 215 " ideal model delta sinusoidal sigma weight residual -30.00 -88.16 58.16 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP B 215 " pdb=" CB ASP B 215 " pdb=" CG ASP B 215 " pdb=" OD1 ASP B 215 " ideal model delta sinusoidal sigma weight residual -30.00 -87.43 57.43 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU C 243 " pdb=" CG GLU C 243 " pdb=" CD GLU C 243 " pdb=" OE1 GLU C 243 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 10093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1663 0.058 - 0.117: 511 0.117 - 0.175: 130 0.175 - 0.233: 23 0.233 - 0.292: 8 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CB VAL A 404 " pdb=" CA VAL A 404 " pdb=" CG1 VAL A 404 " pdb=" CG2 VAL A 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN A 432 " pdb=" N GLN A 432 " pdb=" C GLN A 432 " pdb=" CB GLN A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CG LEU A 309 " pdb=" CB LEU A 309 " pdb=" CD1 LEU A 309 " pdb=" CD2 LEU A 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2332 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 441 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C MET A 441 " -0.070 2.00e-02 2.50e+03 pdb=" O MET A 441 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS A 442 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 82 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C SER C 82 " -0.056 2.00e-02 2.50e+03 pdb=" O SER C 82 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS C 83 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 98 " -0.015 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASN A 98 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN A 98 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR A 99 " -0.018 2.00e-02 2.50e+03 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 186 2.53 - 3.13: 12971 3.13 - 3.72: 28080 3.72 - 4.31: 41755 4.31 - 4.90: 66913 Nonbonded interactions: 149905 Sorted by model distance: nonbonded pdb=" OD2 ASP B 357 " pdb="FE FE B 601 " model vdw 1.942 2.260 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.124 2.260 nonbonded pdb=" OE1 GLN C 191 " pdb=" O1 HCA C 501 " model vdw 2.207 3.040 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.242 2.260 nonbonded pdb=" OD1 ASP D 198 " pdb=" OG1 THR D 301 " model vdw 2.272 3.040 ... (remaining 149900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 2 through 601) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.025 0.753 16495 Z= 1.343 Angle : 1.140 34.376 22236 Z= 0.674 Chirality : 0.062 0.292 2335 Planarity : 0.006 0.044 2857 Dihedral : 13.790 89.710 6430 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.10 % Allowed : 2.44 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.25 (0.18), residues: 1991 helix: 0.59 (0.16), residues: 980 sheet: 0.18 (0.48), residues: 120 loop : -1.02 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 277 TYR 0.046 0.004 TYR A 297 PHE 0.031 0.003 PHE C 429 TRP 0.028 0.004 TRP C 294 HIS 0.014 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.02426 (16479) covalent geometry : angle 1.14021 (22236) hydrogen bonds : bond 0.16110 ( 766) hydrogen bonds : angle 6.69375 ( 2211) Misc. bond : bond 0.24893 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 341 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.2355 (mtm) cc_final: 0.1934 (ppp) REVERT: A 372 MET cc_start: 0.2718 (mmt) cc_final: 0.1968 (mmt) REVERT: A 391 MET cc_start: 0.3616 (tpp) cc_final: 0.2928 (pp-130) REVERT: A 398 THR cc_start: 0.3790 (p) cc_final: 0.3567 (p) REVERT: A 476 GLN cc_start: 0.7820 (tt0) cc_final: 0.7232 (tp40) REVERT: B 23 MET cc_start: 0.5289 (mtt) cc_final: 0.4940 (ptm) REVERT: B 130 ASN cc_start: 0.6886 (m110) cc_final: 0.6413 (m-40) REVERT: B 224 ILE cc_start: 0.8482 (mt) cc_final: 0.8251 (tp) REVERT: B 266 ASP cc_start: 0.7915 (p0) cc_final: 0.7156 (m-30) REVERT: B 503 GLU cc_start: 0.8085 (tt0) cc_final: 0.7641 (tm-30) REVERT: C 205 TRP cc_start: 0.6030 (m100) cc_final: 0.5800 (m-90) REVERT: C 463 MET cc_start: 0.7564 (mmp) cc_final: 0.7313 (mmt) REVERT: D 23 MET cc_start: 0.8012 (ttp) cc_final: 0.7721 (ttt) REVERT: D 93 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6312 (tm-30) REVERT: D 217 VAL cc_start: 0.8211 (t) cc_final: 0.7960 (p) REVERT: D 268 GLN cc_start: 0.6655 (pt0) cc_final: 0.6045 (tm-30) REVERT: D 417 LYS cc_start: 0.6720 (pttm) cc_final: 0.6368 (mmpt) outliers start: 19 outliers final: 1 residues processed: 351 average time/residue: 0.6715 time to fit residues: 259.6615 Evaluate side-chains 195 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 468 ASN B 518 ASN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 468 ASN D 185 HIS D 396 HIS D 513 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.221307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192231 restraints weight = 19163.946| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.64 r_work: 0.4056 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 16495 Z= 0.184 Angle : 0.752 28.892 22236 Z= 0.358 Chirality : 0.047 0.196 2335 Planarity : 0.005 0.048 2857 Dihedral : 4.799 49.424 2518 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.26 % Allowed : 10.34 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.21 (0.18), residues: 1991 helix: 1.14 (0.16), residues: 968 sheet: -0.31 (0.44), residues: 146 loop : -0.90 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.022 0.002 TYR A 446 PHE 0.025 0.002 PHE C 409 TRP 0.021 0.002 TRP A 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00405 (16479) covalent geometry : angle 0.75176 (22236) hydrogen bonds : bond 0.04762 ( 766) hydrogen bonds : angle 5.41229 ( 2211) Misc. bond : bond 0.07813 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.2335 (mtm) cc_final: 0.1836 (ppp) REVERT: A 50 LYS cc_start: 0.5832 (mmmm) cc_final: 0.5517 (mmmm) REVERT: A 139 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: A 369 ASP cc_start: 0.5800 (t0) cc_final: 0.5542 (m-30) REVERT: A 372 MET cc_start: 0.3158 (mmt) cc_final: 0.1789 (mmt) REVERT: A 391 MET cc_start: 0.3719 (tpp) cc_final: 0.2818 (ptt) REVERT: A 398 THR cc_start: 0.4010 (p) cc_final: 0.3795 (p) REVERT: A 476 GLN cc_start: 0.8093 (tt0) cc_final: 0.7657 (tp40) REVERT: B 23 MET cc_start: 0.5488 (mtt) cc_final: 0.5194 (ptm) REVERT: B 101 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 231 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 506 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: C 205 TRP cc_start: 0.6061 (m100) cc_final: 0.5628 (m-90) REVERT: C 277 ARG cc_start: 0.6657 (tpt90) cc_final: 0.6352 (tmt170) REVERT: C 352 MET cc_start: 0.4006 (mtp) cc_final: 0.3634 (mtp) REVERT: C 391 MET cc_start: 0.0873 (tpt) cc_final: 0.0585 (tpp) REVERT: C 464 ASP cc_start: 0.6602 (t70) cc_final: 0.6289 (m-30) REVERT: D 86 MET cc_start: 0.6467 (tpt) cc_final: 0.6020 (mmt) REVERT: D 231 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7805 (tp30) REVERT: D 268 GLN cc_start: 0.6515 (pt0) cc_final: 0.6134 (tm-30) outliers start: 39 outliers final: 7 residues processed: 228 average time/residue: 0.5921 time to fit residues: 151.1108 Evaluate side-chains 189 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 119 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 137 ASN B 338 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN D 185 HIS D 317 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189154 restraints weight = 21361.587| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.63 r_work: 0.4054 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 16495 Z= 0.182 Angle : 0.733 28.989 22236 Z= 0.347 Chirality : 0.046 0.186 2335 Planarity : 0.005 0.053 2857 Dihedral : 4.976 51.499 2514 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.25 % Allowed : 11.79 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.24 (0.18), residues: 1991 helix: 1.27 (0.17), residues: 960 sheet: -0.54 (0.44), residues: 136 loop : -0.94 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 97 TYR 0.021 0.002 TYR B 102 PHE 0.022 0.002 PHE A 429 TRP 0.022 0.002 TRP A 335 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00401 (16479) covalent geometry : angle 0.73261 (22236) hydrogen bonds : bond 0.04869 ( 766) hydrogen bonds : angle 5.26558 ( 2211) Misc. bond : bond 0.08085 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.2431 (mtm) cc_final: 0.1692 (ppp) REVERT: A 50 LYS cc_start: 0.6164 (mmmm) cc_final: 0.5939 (mmmm) REVERT: A 77 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7053 (p0) REVERT: A 123 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6975 (mp) REVERT: A 369 ASP cc_start: 0.6004 (t0) cc_final: 0.5599 (t0) REVERT: A 372 MET cc_start: 0.3671 (mmt) cc_final: 0.2294 (mmt) REVERT: A 391 MET cc_start: 0.4167 (tpp) cc_final: 0.2678 (ptt) REVERT: A 398 THR cc_start: 0.3980 (p) cc_final: 0.3776 (p) REVERT: A 476 GLN cc_start: 0.8066 (tt0) cc_final: 0.7428 (tp-100) REVERT: B 23 MET cc_start: 0.5302 (mtt) cc_final: 0.5046 (ptm) REVERT: B 101 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7636 (m) REVERT: B 131 MET cc_start: 0.7738 (tpt) cc_final: 0.7501 (tpt) REVERT: B 146 MET cc_start: 0.7846 (ttp) cc_final: 0.7496 (ttp) REVERT: B 231 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: B 503 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7952 (tt0) REVERT: B 506 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: C 118 PHE cc_start: 0.6845 (m-10) cc_final: 0.6585 (m-10) REVERT: C 277 ARG cc_start: 0.6901 (tpt90) cc_final: 0.6586 (tmt-80) REVERT: C 394 MET cc_start: 0.2057 (OUTLIER) cc_final: 0.0500 (tpt) REVERT: C 464 ASP cc_start: 0.6585 (t70) cc_final: 0.6307 (m-30) REVERT: D 93 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6538 (tm-30) REVERT: D 231 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8043 (tp30) REVERT: D 246 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 268 GLN cc_start: 0.6478 (pt0) cc_final: 0.5932 (tm-30) REVERT: D 417 LYS cc_start: 0.6668 (pttm) cc_final: 0.5859 (mmtt) REVERT: D 461 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7341 (pp20) outliers start: 56 outliers final: 12 residues processed: 232 average time/residue: 0.6167 time to fit residues: 159.1689 Evaluate side-chains 188 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 169 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.220209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189865 restraints weight = 26048.296| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.83 r_work: 0.4058 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 16495 Z= 0.136 Angle : 0.683 29.075 22236 Z= 0.316 Chirality : 0.044 0.173 2335 Planarity : 0.004 0.052 2857 Dihedral : 4.737 52.802 2514 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.50 % Allowed : 13.88 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.42 (0.19), residues: 1991 helix: 1.42 (0.17), residues: 974 sheet: -0.54 (0.44), residues: 136 loop : -0.88 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 359 TYR 0.027 0.001 TYR A 354 PHE 0.022 0.001 PHE C 409 TRP 0.016 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00290 (16479) covalent geometry : angle 0.68307 (22236) hydrogen bonds : bond 0.04036 ( 766) hydrogen bonds : angle 5.11956 ( 2211) Misc. bond : bond 0.06183 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.2328 (mtm) cc_final: 0.1566 (ppp) REVERT: A 139 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: A 184 GLU cc_start: 0.7691 (mp0) cc_final: 0.7484 (mp0) REVERT: A 299 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.4440 (t80) REVERT: A 369 ASP cc_start: 0.5906 (t0) cc_final: 0.5262 (m-30) REVERT: A 372 MET cc_start: 0.3494 (mmt) cc_final: 0.2250 (mmt) REVERT: A 391 MET cc_start: 0.4245 (tpp) cc_final: 0.2822 (ptt) REVERT: A 476 GLN cc_start: 0.8058 (tt0) cc_final: 0.7398 (tp40) REVERT: B 23 MET cc_start: 0.5283 (mtt) cc_final: 0.4989 (ptm) REVERT: B 130 ASN cc_start: 0.6746 (m110) cc_final: 0.6189 (m-40) REVERT: B 131 MET cc_start: 0.7747 (tpt) cc_final: 0.6865 (tpt) REVERT: B 211 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7587 (mttp) REVERT: B 231 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: B 320 MET cc_start: 0.7956 (mtp) cc_final: 0.7728 (mtt) REVERT: B 503 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8003 (tt0) REVERT: B 506 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 118 PHE cc_start: 0.6811 (m-10) cc_final: 0.6561 (m-10) REVERT: C 139 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: C 205 TRP cc_start: 0.5992 (m100) cc_final: 0.5638 (m-90) REVERT: C 245 MET cc_start: 0.5742 (tmm) cc_final: 0.4953 (tmt) REVERT: C 296 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5682 (tt0) REVERT: C 359 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4957 (mpt180) REVERT: C 394 MET cc_start: 0.2256 (OUTLIER) cc_final: 0.0662 (tpt) REVERT: C 464 ASP cc_start: 0.6695 (t70) cc_final: 0.6463 (m-30) REVERT: D 93 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6697 (tm-30) REVERT: D 241 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8454 (mtmm) REVERT: D 246 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 268 GLN cc_start: 0.6395 (pt0) cc_final: 0.5874 (tm-30) REVERT: D 372 ASP cc_start: 0.7418 (m-30) cc_final: 0.7128 (m-30) REVERT: D 417 LYS cc_start: 0.6761 (pttm) cc_final: 0.5935 (mmtt) REVERT: D 461 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7005 (mm-30) outliers start: 43 outliers final: 10 residues processed: 215 average time/residue: 0.6298 time to fit residues: 150.7365 Evaluate side-chains 187 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 508 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** 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 = 0.4378 r_free = 0.4378 target = 0.215012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184772 restraints weight = 22612.343| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.65 r_work: 0.4008 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 16495 Z= 0.165 Angle : 0.718 29.091 22236 Z= 0.336 Chirality : 0.045 0.187 2335 Planarity : 0.005 0.055 2857 Dihedral : 4.919 56.358 2514 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.25 % Allowed : 13.94 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.34 (0.19), residues: 1991 helix: 1.42 (0.17), residues: 960 sheet: -0.35 (0.42), residues: 146 loop : -1.01 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.016 0.002 TYR B 102 PHE 0.021 0.002 PHE C 409 TRP 0.019 0.001 TRP A 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00364 (16479) covalent geometry : angle 0.71800 (22236) hydrogen bonds : bond 0.04612 ( 766) hydrogen bonds : angle 5.16454 ( 2211) Misc. bond : bond 0.07008 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.2206 (mtm) cc_final: 0.1389 (ppp) REVERT: A 148 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6223 (pt) REVERT: A 184 GLU cc_start: 0.7853 (mp0) cc_final: 0.7548 (mp0) REVERT: A 299 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5037 (t80) REVERT: A 358 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6254 (pt) REVERT: A 369 ASP cc_start: 0.5994 (t0) cc_final: 0.5423 (m-30) REVERT: A 372 MET cc_start: 0.4261 (mmt) cc_final: 0.2435 (mmt) REVERT: A 391 MET cc_start: 0.4107 (tpp) cc_final: 0.2553 (ptt) REVERT: A 476 GLN cc_start: 0.8132 (tt0) cc_final: 0.7552 (tp-100) REVERT: B 23 MET cc_start: 0.5638 (mtt) cc_final: 0.5320 (ptm) REVERT: B 130 ASN cc_start: 0.6817 (m110) cc_final: 0.6382 (m110) REVERT: B 131 MET cc_start: 0.7811 (tpt) cc_final: 0.7205 (tpt) REVERT: B 211 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7675 (mttp) REVERT: B 231 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 320 MET cc_start: 0.8057 (mtp) cc_final: 0.7834 (mtt) REVERT: B 503 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8008 (tt0) REVERT: B 506 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: C 245 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5320 (tmt) REVERT: C 277 ARG cc_start: 0.6841 (tmt-80) cc_final: 0.6600 (tpt170) REVERT: C 296 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5837 (tt0) REVERT: C 359 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4603 (mpt180) REVERT: C 394 MET cc_start: 0.2378 (OUTLIER) cc_final: 0.0655 (tpt) REVERT: D 84 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5751 (mtpt) REVERT: D 93 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6751 (tm-30) REVERT: D 146 MET cc_start: 0.7607 (ptt) cc_final: 0.7338 (ptp) REVERT: D 177 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5963 (m-30) REVERT: D 241 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8577 (mtmm) REVERT: D 268 GLN cc_start: 0.6497 (pt0) cc_final: 0.5998 (tm-30) REVERT: D 417 LYS cc_start: 0.6835 (pttm) cc_final: 0.6082 (mmtt) REVERT: D 461 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7241 (mm-30) outliers start: 56 outliers final: 17 residues processed: 219 average time/residue: 0.6190 time to fit residues: 151.0012 Evaluate side-chains 195 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 508 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 133 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 137 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.210549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180760 restraints weight = 20947.978| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.56 r_work: 0.3969 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 16495 Z= 0.217 Angle : 0.780 29.096 22236 Z= 0.374 Chirality : 0.048 0.210 2335 Planarity : 0.005 0.059 2857 Dihedral : 5.385 56.675 2514 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.48 % Allowed : 14.52 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.04 (0.18), residues: 1991 helix: 1.04 (0.17), residues: 962 sheet: -0.59 (0.41), residues: 144 loop : -1.11 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 242 TYR 0.026 0.002 TYR A 354 PHE 0.022 0.002 PHE A 429 TRP 0.038 0.002 TRP C 335 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00497 (16479) covalent geometry : angle 0.78050 (22236) hydrogen bonds : bond 0.05387 ( 766) hydrogen bonds : angle 5.37584 ( 2211) Misc. bond : bond 0.07852 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 188 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.1873 (mtm) cc_final: 0.0793 (ppp) REVERT: A 123 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7127 (mp) REVERT: A 148 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6220 (pt) REVERT: A 299 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5839 (m-10) REVERT: A 343 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6911 (mtp-110) REVERT: A 355 ILE cc_start: 0.5904 (mm) cc_final: 0.5584 (mt) REVERT: A 358 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6144 (pt) REVERT: A 369 ASP cc_start: 0.6201 (t0) cc_final: 0.5598 (m-30) REVERT: A 372 MET cc_start: 0.4823 (mmt) cc_final: 0.4588 (mpt) REVERT: A 391 MET cc_start: 0.4409 (tpp) cc_final: 0.2737 (ptt) REVERT: A 476 GLN cc_start: 0.8197 (tt0) cc_final: 0.7623 (tp-100) REVERT: B 23 MET cc_start: 0.5706 (mtt) cc_final: 0.5412 (ptm) REVERT: B 130 ASN cc_start: 0.6923 (m110) cc_final: 0.6371 (m-40) REVERT: B 211 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7648 (mttp) REVERT: B 231 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 320 MET cc_start: 0.8169 (mtp) cc_final: 0.7890 (mtt) REVERT: B 503 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8075 (tt0) REVERT: B 506 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: C 96 ARG cc_start: 0.7841 (mpt90) cc_final: 0.7135 (mmt-90) REVERT: C 245 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5273 (tmt) REVERT: C 296 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: C 320 ILE cc_start: 0.5236 (mt) cc_final: 0.4725 (mp) REVERT: C 359 ARG cc_start: 0.5226 (OUTLIER) cc_final: 0.3091 (mpp-170) REVERT: C 394 MET cc_start: 0.2621 (OUTLIER) cc_final: 0.0870 (tpt) REVERT: D 84 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5832 (mtpt) REVERT: D 93 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6755 (tm-30) REVERT: D 177 ASP cc_start: 0.6355 (OUTLIER) cc_final: 0.5996 (m-30) REVERT: D 262 ASP cc_start: 0.8228 (t0) cc_final: 0.7797 (t0) REVERT: D 268 GLN cc_start: 0.6537 (pt0) cc_final: 0.6018 (tm-30) REVERT: D 372 ASP cc_start: 0.7534 (m-30) cc_final: 0.7299 (m-30) REVERT: D 417 LYS cc_start: 0.6944 (pttm) cc_final: 0.6139 (mmtt) REVERT: D 461 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7508 (pp20) outliers start: 60 outliers final: 20 residues processed: 229 average time/residue: 0.6407 time to fit residues: 163.2618 Evaluate side-chains 201 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 6 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.214028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183240 restraints weight = 27180.195| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.83 r_work: 0.3987 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 16495 Z= 0.145 Angle : 0.711 29.090 22236 Z= 0.332 Chirality : 0.044 0.179 2335 Planarity : 0.005 0.057 2857 Dihedral : 5.029 58.250 2514 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.61 % Allowed : 15.97 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.18), residues: 1991 helix: 1.30 (0.17), residues: 964 sheet: -0.95 (0.40), residues: 154 loop : -0.98 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.024 0.002 TYR A 290 PHE 0.021 0.001 PHE C 409 TRP 0.050 0.001 TRP C 335 HIS 0.011 0.001 HIS C 383 Details of bonding type rmsd covalent geometry : bond 0.00315 (16479) covalent geometry : angle 0.71085 (22236) hydrogen bonds : bond 0.04311 ( 766) hydrogen bonds : angle 5.17557 ( 2211) Misc. bond : bond 0.06196 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.1767 (mtm) cc_final: 0.1112 (ppp) REVERT: A 139 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: A 148 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6168 (pt) REVERT: A 184 GLU cc_start: 0.7792 (mp0) cc_final: 0.7505 (mp0) REVERT: A 289 LYS cc_start: 0.5202 (tmmt) cc_final: 0.4644 (tttt) REVERT: A 299 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5881 (m-10) REVERT: A 343 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6814 (mtp-110) REVERT: A 372 MET cc_start: 0.4708 (mmt) cc_final: 0.4312 (mpt) REVERT: A 391 MET cc_start: 0.4379 (tpp) cc_final: 0.2777 (ptt) REVERT: A 421 ILE cc_start: 0.6858 (mt) cc_final: 0.6641 (mt) REVERT: A 476 GLN cc_start: 0.8223 (tt0) cc_final: 0.7619 (tp40) REVERT: B 23 MET cc_start: 0.5708 (mtt) cc_final: 0.5417 (ptm) REVERT: B 130 ASN cc_start: 0.6859 (m110) cc_final: 0.6315 (m-40) REVERT: B 142 TYR cc_start: 0.7351 (m-80) cc_final: 0.6951 (m-80) REVERT: B 211 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7631 (mttp) REVERT: B 220 SER cc_start: 0.8001 (p) cc_final: 0.7758 (m) REVERT: B 231 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: B 320 MET cc_start: 0.8081 (mtp) cc_final: 0.7809 (mtt) REVERT: B 503 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8101 (tt0) REVERT: B 506 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: C 96 ARG cc_start: 0.7775 (mpt90) cc_final: 0.7152 (mmt-90) REVERT: C 118 PHE cc_start: 0.6895 (m-10) cc_final: 0.6682 (m-10) REVERT: C 245 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5421 (tmt) REVERT: C 277 ARG cc_start: 0.6927 (tpt170) cc_final: 0.6542 (tmt-80) REVERT: C 296 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5714 (mp0) REVERT: C 359 ARG cc_start: 0.5142 (OUTLIER) cc_final: 0.2862 (mpp-170) REVERT: D 84 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5865 (mtpt) REVERT: D 93 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6779 (tm-30) REVERT: D 177 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.6059 (m-30) REVERT: D 262 ASP cc_start: 0.8134 (t0) cc_final: 0.7672 (t0) REVERT: D 268 GLN cc_start: 0.6431 (pt0) cc_final: 0.5923 (tm-30) REVERT: D 372 ASP cc_start: 0.7530 (m-30) cc_final: 0.7194 (m-30) REVERT: D 417 LYS cc_start: 0.7043 (pttm) cc_final: 0.6215 (mmtt) REVERT: D 461 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7482 (pp20) outliers start: 45 outliers final: 15 residues processed: 209 average time/residue: 0.6155 time to fit residues: 143.8297 Evaluate side-chains 196 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN B 137 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.214035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184459 restraints weight = 23186.451| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.65 r_work: 0.4005 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 16495 Z= 0.143 Angle : 0.706 29.113 22236 Z= 0.328 Chirality : 0.044 0.190 2335 Planarity : 0.004 0.056 2857 Dihedral : 4.898 59.985 2514 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.73 % Allowed : 15.91 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1991 helix: 1.38 (0.17), residues: 964 sheet: -0.82 (0.41), residues: 156 loop : -0.94 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.020 0.002 TYR A 290 PHE 0.022 0.001 PHE C 409 TRP 0.051 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00309 (16479) covalent geometry : angle 0.70612 (22236) hydrogen bonds : bond 0.04206 ( 766) hydrogen bonds : angle 5.13400 ( 2211) Misc. bond : bond 0.06113 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.1664 (mtm) cc_final: 0.0640 (ppp) REVERT: A 139 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 148 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6184 (pt) REVERT: A 358 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5943 (pt) REVERT: A 372 MET cc_start: 0.4700 (mmt) cc_final: 0.4350 (mpt) REVERT: A 391 MET cc_start: 0.4166 (tpp) cc_final: 0.2567 (ptt) REVERT: A 421 ILE cc_start: 0.6813 (mt) cc_final: 0.6578 (mt) REVERT: A 474 LYS cc_start: 0.8343 (mmtp) cc_final: 0.8132 (mmtp) REVERT: A 476 GLN cc_start: 0.8177 (tt0) cc_final: 0.7587 (tp40) REVERT: B 130 ASN cc_start: 0.6849 (m110) cc_final: 0.6268 (m-40) REVERT: B 142 TYR cc_start: 0.7311 (m-80) cc_final: 0.6979 (m-80) REVERT: B 211 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7644 (mttp) REVERT: B 220 SER cc_start: 0.8031 (p) cc_final: 0.7758 (m) REVERT: B 231 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: B 266 ASP cc_start: 0.7954 (p0) cc_final: 0.7753 (p0) REVERT: B 320 MET cc_start: 0.8059 (mtp) cc_final: 0.7780 (mtt) REVERT: B 503 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8077 (tt0) REVERT: B 506 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: C 96 ARG cc_start: 0.7741 (mpt90) cc_final: 0.7133 (mmt-90) REVERT: C 118 PHE cc_start: 0.6768 (m-10) cc_final: 0.6567 (m-10) REVERT: C 123 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7436 (mp) REVERT: C 277 ARG cc_start: 0.7009 (tpt170) cc_final: 0.6738 (tmt-80) REVERT: C 296 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5695 (mp0) REVERT: C 322 LYS cc_start: 0.6717 (tttm) cc_final: 0.6333 (ttmt) REVERT: C 339 VAL cc_start: 0.6682 (t) cc_final: 0.6433 (m) REVERT: C 359 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.2422 (mpp-170) REVERT: D 93 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6790 (tm-30) REVERT: D 177 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: D 262 ASP cc_start: 0.8131 (t0) cc_final: 0.7657 (t0) REVERT: D 268 GLN cc_start: 0.6423 (pt0) cc_final: 0.5913 (tm-30) REVERT: D 372 ASP cc_start: 0.7496 (m-30) cc_final: 0.7189 (m-30) REVERT: D 417 LYS cc_start: 0.7027 (pttm) cc_final: 0.6215 (mmtt) REVERT: D 461 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7282 (mm-30) outliers start: 47 outliers final: 18 residues processed: 220 average time/residue: 0.6212 time to fit residues: 152.1404 Evaluate side-chains 202 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 508 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 271 ASN C 383 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.210837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.181553 restraints weight = 21169.056| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.57 r_work: 0.3979 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 16495 Z= 0.190 Angle : 0.763 29.113 22236 Z= 0.363 Chirality : 0.046 0.200 2335 Planarity : 0.005 0.058 2857 Dihedral : 5.147 59.008 2514 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.50 % Allowed : 16.90 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.02 (0.18), residues: 1991 helix: 1.18 (0.17), residues: 964 sheet: -0.86 (0.43), residues: 134 loop : -1.14 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 439 TYR 0.027 0.002 TYR A 290 PHE 0.021 0.002 PHE C 459 TRP 0.058 0.002 TRP C 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00429 (16479) covalent geometry : angle 0.76348 (22236) hydrogen bonds : bond 0.04959 ( 766) hydrogen bonds : angle 5.27920 ( 2211) Misc. bond : bond 0.06982 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.1664 (mtm) cc_final: 0.0458 (ppp) REVERT: A 15 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6403 (mp0) REVERT: A 23 LYS cc_start: 0.6088 (tppt) cc_final: 0.5064 (pttt) REVERT: A 139 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: A 148 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6216 (pt) REVERT: A 358 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.5899 (pt) REVERT: A 372 MET cc_start: 0.4997 (mmt) cc_final: 0.4783 (mpt) REVERT: A 389 ARG cc_start: 0.4136 (mtt90) cc_final: 0.3527 (mmt90) REVERT: A 391 MET cc_start: 0.4274 (tpp) cc_final: 0.2574 (ptt) REVERT: A 394 MET cc_start: 0.5063 (pmm) cc_final: 0.3059 (tpt) REVERT: A 421 ILE cc_start: 0.6889 (mt) cc_final: 0.6630 (mt) REVERT: A 474 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8232 (mmtp) REVERT: A 476 GLN cc_start: 0.8192 (tt0) cc_final: 0.7614 (tp40) REVERT: B 130 ASN cc_start: 0.6876 (m110) cc_final: 0.6332 (m-40) REVERT: B 142 TYR cc_start: 0.7374 (m-80) cc_final: 0.6967 (m-80) REVERT: B 211 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7643 (mttp) REVERT: B 231 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 320 MET cc_start: 0.8123 (mtp) cc_final: 0.7847 (mtt) REVERT: B 503 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8064 (tt0) REVERT: B 506 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: C 96 ARG cc_start: 0.7815 (mpt90) cc_final: 0.7140 (mmt-90) REVERT: C 123 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7507 (mp) REVERT: C 196 HIS cc_start: 0.4905 (t70) cc_final: 0.4206 (t70) REVERT: C 277 ARG cc_start: 0.7045 (tpt170) cc_final: 0.6747 (tmt-80) REVERT: C 296 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5785 (mp0) REVERT: C 320 ILE cc_start: 0.5312 (mt) cc_final: 0.4887 (mp) REVERT: C 322 LYS cc_start: 0.6692 (tttm) cc_final: 0.6257 (ttmt) REVERT: C 359 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.2473 (mpp-170) REVERT: C 408 GLU cc_start: 0.3085 (mt-10) cc_final: 0.1697 (tp30) REVERT: D 93 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6771 (tm-30) REVERT: D 177 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5982 (m-30) REVERT: D 262 ASP cc_start: 0.8179 (t0) cc_final: 0.7717 (t0) REVERT: D 268 GLN cc_start: 0.6418 (pt0) cc_final: 0.5893 (tm-30) REVERT: D 417 LYS cc_start: 0.7014 (pttm) cc_final: 0.6246 (mmtt) REVERT: D 461 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7506 (pp20) outliers start: 43 outliers final: 18 residues processed: 218 average time/residue: 0.6492 time to fit residues: 156.8605 Evaluate side-chains 201 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 HIS ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** 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 = 0.4358 r_free = 0.4358 target = 0.212638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182055 restraints weight = 27702.965| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.83 r_work: 0.3978 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 16495 Z= 0.158 Angle : 0.738 29.098 22236 Z= 0.348 Chirality : 0.044 0.192 2335 Planarity : 0.005 0.056 2857 Dihedral : 5.007 56.934 2514 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.09 % Allowed : 17.60 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.09 (0.18), residues: 1991 helix: 1.26 (0.17), residues: 966 sheet: -1.10 (0.42), residues: 144 loop : -1.08 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 439 TYR 0.016 0.002 TYR A 354 PHE 0.028 0.002 PHE C 459 TRP 0.061 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00351 (16479) covalent geometry : angle 0.73804 (22236) hydrogen bonds : bond 0.04470 ( 766) hydrogen bonds : angle 5.21059 ( 2211) Misc. bond : bond 0.06226 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.1540 (mtm) cc_final: 0.0262 (ppp) REVERT: A 15 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6559 (mp0) REVERT: A 23 LYS cc_start: 0.5696 (tppt) cc_final: 0.4784 (pttt) REVERT: A 139 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: A 148 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6157 (pt) REVERT: A 263 GLU cc_start: 0.6027 (pm20) cc_final: 0.5296 (pm20) REVERT: A 358 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5860 (pt) REVERT: A 372 MET cc_start: 0.5102 (mmt) cc_final: 0.4797 (mpt) REVERT: A 389 ARG cc_start: 0.4201 (mtt90) cc_final: 0.3602 (mmt90) REVERT: A 391 MET cc_start: 0.4256 (tpp) cc_final: 0.2463 (ptt) REVERT: A 394 MET cc_start: 0.4830 (pmm) cc_final: 0.3179 (tpt) REVERT: A 421 ILE cc_start: 0.6948 (mt) cc_final: 0.6724 (mt) REVERT: A 474 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8223 (mmtp) REVERT: A 476 GLN cc_start: 0.8195 (tt0) cc_final: 0.7618 (tp40) REVERT: B 130 ASN cc_start: 0.6929 (m110) cc_final: 0.6394 (m-40) REVERT: B 142 TYR cc_start: 0.7309 (m-80) cc_final: 0.6965 (m-80) REVERT: B 211 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7608 (mttp) REVERT: B 231 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: B 320 MET cc_start: 0.8098 (mtp) cc_final: 0.7829 (mtt) REVERT: B 389 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: B 503 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8120 (tt0) REVERT: B 506 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: C 12 LEU cc_start: -0.1659 (OUTLIER) cc_final: -0.1921 (pp) REVERT: C 96 ARG cc_start: 0.7812 (mpt90) cc_final: 0.7188 (mmt-90) REVERT: C 118 PHE cc_start: 0.6884 (m-10) cc_final: 0.6656 (m-10) REVERT: C 123 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7539 (mp) REVERT: C 196 HIS cc_start: 0.4968 (t70) cc_final: 0.4270 (t70) REVERT: C 205 TRP cc_start: 0.6147 (m100) cc_final: 0.5912 (m-90) REVERT: C 209 LYS cc_start: 0.5303 (tttp) cc_final: 0.5083 (mmpt) REVERT: C 277 ARG cc_start: 0.7038 (tpt170) cc_final: 0.6655 (tmt-80) REVERT: C 295 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.4889 (tpp) REVERT: C 296 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5487 (mp0) REVERT: C 352 MET cc_start: 0.4438 (mtp) cc_final: 0.4214 (ttm) REVERT: C 359 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.2403 (mpp-170) REVERT: C 408 GLU cc_start: 0.3053 (mt-10) cc_final: 0.1651 (tp30) REVERT: D 93 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6752 (tm-30) REVERT: D 177 ASP cc_start: 0.6419 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: D 262 ASP cc_start: 0.8179 (t0) cc_final: 0.7659 (t0) REVERT: D 268 GLN cc_start: 0.6435 (pt0) cc_final: 0.5935 (tm-30) REVERT: D 417 LYS cc_start: 0.7068 (pttm) cc_final: 0.6279 (mmtt) REVERT: D 461 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7540 (pp20) outliers start: 36 outliers final: 18 residues processed: 209 average time/residue: 0.6304 time to fit residues: 146.3145 Evaluate side-chains 201 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 508 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 57 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 13 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 513 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 = 0.4388 r_free = 0.4388 target = 0.215412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186723 restraints weight = 27798.430| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.68 r_work: 0.4027 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 16495 Z= 0.132 Angle : 0.711 29.111 22236 Z= 0.332 Chirality : 0.043 0.175 2335 Planarity : 0.004 0.054 2857 Dihedral : 4.738 55.177 2514 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.86 % Allowed : 18.06 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1991 helix: 1.37 (0.17), residues: 980 sheet: -0.88 (0.43), residues: 140 loop : -0.97 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.027 0.001 TYR A 290 PHE 0.025 0.001 PHE C 459 TRP 0.055 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00283 (16479) covalent geometry : angle 0.71115 (22236) hydrogen bonds : bond 0.03933 ( 766) hydrogen bonds : angle 5.09159 ( 2211) Misc. bond : bond 0.05542 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7016.74 seconds wall clock time: 120 minutes 13.79 seconds (7213.79 seconds total)