Starting phenix.real_space_refine on Fri Aug 7 23:46:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx4_54357/08_2026/9rx4_54357.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 5 5.49 5 Mg 2 5.21 5 S 126 5.16 5 C 15128 2.51 5 N 4137 2.21 5 O 4475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23875 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6546 Classifications: {'peptide': 810} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 770} Chain breaks: 2 Chain: "B" Number of atoms: 9703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9703 Classifications: {'peptide': 1220} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1160} Chain breaks: 5 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2773 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 6, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2527 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 2 Chain: "E" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1368 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 807 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' MG': 1, 'MYR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16468 SG CYS C 137 43.121 132.815 33.941 1.00154.99 S ATOM 16492 SG CYS C 140 45.339 133.277 35.681 1.00146.60 S ATOM 19060 SG CYS D 43 45.576 129.342 33.510 1.00127.35 S ATOM 19081 SG CYS D 46 43.486 129.741 35.119 1.00144.96 S ATOM 19157 SG CYS D 55 51.937 135.564 22.359 1.00139.80 S ATOM 19177 SG CYS D 58 51.574 138.332 22.696 1.00141.01 S ATOM 22941 SG CYS I 18 48.159 135.580 21.970 1.00142.91 S ATOM 22967 SG CYS I 21 50.464 136.477 19.784 1.00136.16 S Time building chain proxies: 5.00, per 1000 atoms: 0.21 Number of scatterers: 23875 At special positions: 0 Unit cell: (103.2, 182.32, 231.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 126 16.00 P 5 15.00 Mg 2 11.99 O 4475 8.00 N 4137 7.00 C 15128 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS D 46 " pdb="ZN ZN C 501 " - pdb=" SG CYS D 43 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" SG CYS I 18 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 501 " - pdb=" SG CYS I 21 " Number of angles added : 12 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5626 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 22 sheets defined 53.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.741A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 170 through 184 removed outlier: 4.025A pdb=" N LYS A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 removed outlier: 3.676A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 removed outlier: 3.932A pdb=" N SER A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.969A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.725A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLU A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 328 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.709A pdb=" N PHE A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 removed outlier: 3.630A pdb=" N ALA A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.692A pdb=" N LEU A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 367 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 368 " --> pdb=" O GLU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 368' Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.565A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.515A pdb=" N GLN A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.815A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 529 removed outlier: 3.751A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.514A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.517A pdb=" N LYS A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.605A pdb=" N GLN A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 removed outlier: 3.705A pdb=" N ASP A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.736A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 739 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.651A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 811 removed outlier: 3.850A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 4.177A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.678A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.604A pdb=" N LYS A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 868 removed outlier: 3.653A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.531A pdb=" N ILE B 13 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.565A pdb=" N PHE B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP B 22 " --> pdb=" O TYR B 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 22' Processing helix chain 'B' and resid 64 through 78 removed outlier: 4.022A pdb=" N LYS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.756A pdb=" N ILE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 115' Processing helix chain 'B' and resid 121 through 141 removed outlier: 3.677A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.074A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.569A pdb=" N ASN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.562A pdb=" N ASN B 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.780A pdb=" N ARG B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.546A pdb=" N TYR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.161A pdb=" N TYR B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.581A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 removed outlier: 3.996A pdb=" N LYS B 333 " --> pdb=" O GLN B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.658A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 removed outlier: 3.739A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.521A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.915A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 409 Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 418 through 425 removed outlier: 3.806A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.694A pdb=" N LEU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 457 through 467 removed outlier: 4.051A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Proline residue: B 465 - end of helix Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.969A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.620A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 510 removed outlier: 3.761A pdb=" N GLU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.715A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 4.176A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 558 " --> pdb=" O GLN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.736A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 583 removed outlier: 4.227A pdb=" N LYS B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 578 " --> pdb=" O ASN B 574 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 removed outlier: 3.714A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.059A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 615 removed outlier: 3.727A pdb=" N SER B 613 " --> pdb=" O TRP B 610 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 614 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 610 through 615' Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.550A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.587A pdb=" N GLY B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 4.048A pdb=" N VAL B 653 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.706A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.990A pdb=" N ARG B 672 " --> pdb=" O ASN B 668 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 removed outlier: 4.451A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.529A pdb=" N ARG B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 781 through 790 removed outlier: 4.227A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 786 " --> pdb=" O GLU B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.789A pdb=" N GLN B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 809 " --> pdb=" O VAL B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 812 No H-bonds generated for 'chain 'B' and resid 810 through 812' Processing helix chain 'B' and resid 938 through 962 removed outlier: 4.016A pdb=" N THR B 942 " --> pdb=" O THR B 938 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 968 removed outlier: 5.081A pdb=" N GLU B 966 " --> pdb=" O GLN B 963 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 967 " --> pdb=" O MET B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.859A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B1142 " --> pdb=" O LEU B1139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1138 through 1142' Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'B' and resid 1284 through 1286 No H-bonds generated for 'chain 'B' and resid 1284 through 1286' Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.934A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 170 removed outlier: 4.069A pdb=" N LEU C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 removed outlier: 3.869A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 217 Processing helix chain 'C' and resid 218 through 260 removed outlier: 4.257A pdb=" N GLU C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 4.039A pdb=" N LYS C 266 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 267 " --> pdb=" O LEU C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 267' Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.660A pdb=" N PHE C 274 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.796A pdb=" N ILE C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 363 through 384 removed outlier: 3.585A pdb=" N CYS C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 447 removed outlier: 3.519A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C 446 " --> pdb=" O TRP C 442 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.634A pdb=" N VAL D 59 " --> pdb=" O CYS D 55 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.523A pdb=" N LEU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 177 removed outlier: 3.524A pdb=" N MET D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 205 removed outlier: 3.746A pdb=" N LEU D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 removed outlier: 3.696A pdb=" N ALA D 278 " --> pdb=" O ASP D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 278' Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 297 through 322 removed outlier: 4.242A pdb=" N TYR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.561A pdb=" N PHE D 334 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 362 removed outlier: 3.632A pdb=" N GLN D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.622A pdb=" N PHE E 73 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 removed outlier: 4.000A pdb=" N PHE E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.586A pdb=" N GLN E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 144 removed outlier: 3.714A pdb=" N ALA E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 169 removed outlier: 3.536A pdb=" N SER E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 176 removed outlier: 3.986A pdb=" N LYS E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 23 removed outlier: 3.653A pdb=" N LEU L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA L 23 " --> pdb=" O ASP L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 42 removed outlier: 3.611A pdb=" N ALA L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 32 " --> pdb=" O GLU L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 91 removed outlier: 4.217A pdb=" N LEU L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER L 56 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP L 91 " --> pdb=" O GLN L 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 4.118A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 109 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 11.203A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 139 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 221 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 145 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.775A pdb=" N ILE A 591 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 603 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 610 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.775A pdb=" N ILE A 591 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 603 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 623 " --> pdb=" O TYR A 631 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.196A pdb=" N SER B 31 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG B 42 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 33 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 102 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.396A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 984 through 989 removed outlier: 5.997A pdb=" N LEU B 985 " --> pdb=" O LYS B1358 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS B1358 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 987 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B1356 " --> pdb=" O ALA B 987 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B1345 " --> pdb=" O TRP B1357 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B1338 " --> pdb=" O PHE B1344 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 996 through 1001 removed outlier: 4.136A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B1008 " --> pdb=" O TRP B1020 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1045 through 1051 removed outlier: 7.139A pdb=" N ALA B1060 " --> pdb=" O LYS B1046 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B1048 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B1058 " --> pdb=" O LEU B1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B1050 " --> pdb=" O TYR B1056 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TYR B1056 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B1086 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B1070 " --> pdb=" O PRO B1084 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1100 through 1105 removed outlier: 4.064A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B1111 " --> pdb=" O PHE B1104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 4.075A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1166 " --> pdb=" O ILE B1158 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET B1165 " --> pdb=" O SER B1178 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER B1178 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N CYS B1167 " --> pdb=" O ILE B1176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.346A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1242 through 1248 removed outlier: 3.501A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B1248 " --> pdb=" O ILE B1255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 276 through 279 removed outlier: 4.236A pdb=" N GLY C 283 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 331 removed outlier: 4.428A pdb=" N LEU C 349 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 396 through 397 removed outlier: 4.082A pdb=" N TYR C 413 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AC4, first strand: chain 'E' and resid 47 through 55 removed outlier: 6.560A pdb=" N TYR E 10 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLN E 63 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE E 12 " --> pdb=" O GLN E 63 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP E 65 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 14 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 88 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU E 15 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL E 90 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 17 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASP E 92 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 87 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL E 122 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL E 89 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN E 124 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR E 91 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LEU E 151 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU E 121 " --> pdb=" O LEU E 151 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 3036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7787 1.34 - 1.46: 4366 1.46 - 1.58: 11990 1.58 - 1.69: 8 1.69 - 1.81: 198 Bond restraints: 24349 Sorted by residual: bond pdb=" C LYS B 650 " pdb=" N PRO B 651 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" C ALA B 406 " pdb=" N PRO B 407 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.30e+00 bond pdb=" CA VAL B1310 " pdb=" CB VAL B1310 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.56e+00 bond pdb=" CA LYS B 650 " pdb=" C LYS B 650 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.00e+00 bond pdb=" CA THR B 419 " pdb=" C THR B 419 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.26e-02 6.30e+03 1.99e+00 ... (remaining 24344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 32775 3.92 - 7.83: 104 7.83 - 11.74: 10 11.74 - 15.66: 2 15.66 - 19.57: 1 Bond angle restraints: 32892 Sorted by residual: angle pdb=" N VAL B 719 " pdb=" CA VAL B 719 " pdb=" C VAL B 719 " ideal model delta sigma weight residual 113.71 107.75 5.96 9.50e-01 1.11e+00 3.94e+01 angle pdb=" CA LEU A 471 " pdb=" CB LEU A 471 " pdb=" CG LEU A 471 " ideal model delta sigma weight residual 116.30 135.87 -19.57 3.50e+00 8.16e-02 3.13e+01 angle pdb=" C VAL B 719 " pdb=" CA VAL B 719 " pdb=" CB VAL B 719 " ideal model delta sigma weight residual 110.63 115.22 -4.59 9.40e-01 1.13e+00 2.39e+01 angle pdb=" N PRO B1286 " pdb=" CA PRO B1286 " pdb=" C PRO B1286 " ideal model delta sigma weight residual 112.47 122.06 -9.59 2.06e+00 2.36e-01 2.17e+01 angle pdb=" N LYS B 650 " pdb=" CA LYS B 650 " pdb=" C LYS B 650 " ideal model delta sigma weight residual 109.81 119.62 -9.81 2.21e+00 2.05e-01 1.97e+01 ... (remaining 32887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.80: 14265 30.80 - 61.60: 534 61.60 - 92.40: 49 92.40 - 123.20: 1 123.20 - 154.00: 3 Dihedral angle restraints: 14852 sinusoidal: 6188 harmonic: 8664 Sorted by residual: dihedral pdb=" C8 GTP E 301 " pdb=" C1' GTP E 301 " pdb=" N9 GTP E 301 " pdb=" O4' GTP E 301 " ideal model delta sinusoidal sigma weight residual 104.59 -49.41 154.00 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O5' GTP E 301 " pdb=" O3A GTP E 301 " pdb=" PA GTP E 301 " pdb=" PB GTP E 301 " ideal model delta sinusoidal sigma weight residual 274.12 128.25 145.87 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' GTP E 301 " pdb=" O5' GTP E 301 " pdb=" PA GTP E 301 " pdb=" O3A GTP E 301 " ideal model delta sinusoidal sigma weight residual 69.27 -60.18 129.45 1 2.00e+01 2.50e-03 3.92e+01 ... (remaining 14849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3051 0.060 - 0.121: 532 0.121 - 0.181: 54 0.181 - 0.242: 3 0.242 - 0.302: 4 Chirality restraints: 3644 Sorted by residual: chirality pdb=" CB VAL B1310 " pdb=" CA VAL B1310 " pdb=" CG1 VAL B1310 " pdb=" CG2 VAL B1310 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PRO B1286 " pdb=" N PRO B1286 " pdb=" C PRO B1286 " pdb=" CB PRO B1286 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LYS B 650 " pdb=" N LYS B 650 " pdb=" C LYS B 650 " pdb=" CB LYS B 650 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3641 not shown) Planarity restraints: 4213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B1285 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO B1286 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B1286 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B1286 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 661 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO B 662 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 662 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 662 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 280 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 281 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.031 5.00e-02 4.00e+02 ... (remaining 4210 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 154 2.62 - 3.19: 18409 3.19 - 3.76: 33882 3.76 - 4.33: 44691 4.33 - 4.90: 75826 Nonbonded interactions: 172962 Sorted by model distance: nonbonded pdb=" OG1 THR E 43 " pdb="MG MG E 302 " model vdw 2.045 2.170 nonbonded pdb=" OG SER E 25 " pdb="MG MG E 302 " model vdw 2.105 2.170 nonbonded pdb=" O ARG C 255 " pdb=" OG1 THR C 259 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR C 333 " pdb=" OG1 THR D 302 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASP B 690 " pdb=" OH TYR C 162 " model vdw 2.295 3.040 ... (remaining 172957 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.550 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.004 0.104 24358 Z= 0.211 Angle : 0.896 50.156 32904 Z= 0.399 Chirality : 0.047 0.302 3644 Planarity : 0.006 0.105 4213 Dihedral : 15.736 154.001 9226 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 0.15 % Allowed : 10.71 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -1.55 (0.14), residues: 2920 helix: -0.75 (0.13), residues: 1292 sheet: 0.30 (0.29), residues: 314 loop : -1.57 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.021 0.002 TYR A 803 PHE 0.024 0.002 PHE B 130 TRP 0.016 0.002 TRP B1155 HIS 0.005 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (24349) covalent geometry : angle 0.70931 / 0.39 (32892) hydrogen bonds : bond 0.20097 / 12.90 ( 1050) hydrogen bonds : angle 5.97161 / 4.05 ( 3036) metal coordination : bond 0.05617 / 3.81 ( 8) metal coordination : angle 28.67901 / 14.67 ( 12) Misc. bond : bond 0.10358 / 6.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 756 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8819 (ttm) cc_final: 0.8448 (ttm) REVERT: A 194 ASP cc_start: 0.7854 (m-30) cc_final: 0.7488 (m-30) REVERT: A 346 LYS cc_start: 0.8844 (tttt) cc_final: 0.8482 (mmtm) REVERT: A 350 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8530 (mm-30) REVERT: A 358 MET cc_start: 0.7953 (ptm) cc_final: 0.7468 (ptt) REVERT: A 362 ASP cc_start: 0.7985 (m-30) cc_final: 0.7677 (p0) REVERT: A 370 HIS cc_start: 0.8285 (m-70) cc_final: 0.8021 (t-170) REVERT: A 372 THR cc_start: 0.8438 (p) cc_final: 0.8173 (t) REVERT: A 385 ARG cc_start: 0.5065 (ptp-170) cc_final: 0.4853 (ptp90) REVERT: A 486 ASN cc_start: 0.8527 (t0) cc_final: 0.8183 (t0) REVERT: A 505 ASP cc_start: 0.8204 (t0) cc_final: 0.7475 (t0) REVERT: A 516 MET cc_start: 0.8294 (tmm) cc_final: 0.7065 (tmm) REVERT: A 517 TYR cc_start: 0.7738 (m-10) cc_final: 0.6930 (m-10) REVERT: A 576 LEU cc_start: 0.8053 (mp) cc_final: 0.7683 (tp) REVERT: A 577 LEU cc_start: 0.8292 (mt) cc_final: 0.7976 (mm) REVERT: A 601 ILE cc_start: 0.8425 (pp) cc_final: 0.8177 (mm) REVERT: A 611 LEU cc_start: 0.8601 (mt) cc_final: 0.8373 (pt) REVERT: A 620 GLN cc_start: 0.8503 (tt0) cc_final: 0.8257 (tm-30) REVERT: A 622 PHE cc_start: 0.8581 (m-80) cc_final: 0.7986 (m-80) REVERT: A 624 LYS cc_start: 0.7164 (mttt) cc_final: 0.6946 (ptmm) REVERT: A 636 LYS cc_start: 0.8527 (mttt) cc_final: 0.7988 (mttp) REVERT: A 656 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8563 (tttt) REVERT: A 678 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8433 (mmmm) REVERT: A 688 VAL cc_start: 0.8938 (t) cc_final: 0.8663 (p) REVERT: A 795 TYR cc_start: 0.7624 (t80) cc_final: 0.7225 (t80) REVERT: A 796 GLN cc_start: 0.7627 (mm110) cc_final: 0.7425 (mp10) REVERT: A 830 ASP cc_start: 0.7968 (m-30) cc_final: 0.7630 (m-30) REVERT: A 836 ASP cc_start: 0.8229 (p0) cc_final: 0.7697 (p0) REVERT: A 849 ASP cc_start: 0.8315 (p0) cc_final: 0.7935 (p0) REVERT: B 17 GLU cc_start: 0.7856 (tt0) cc_final: 0.7563 (tm-30) REVERT: B 40 VAL cc_start: 0.8405 (t) cc_final: 0.8177 (m) REVERT: B 121 ASN cc_start: 0.8097 (m-40) cc_final: 0.7870 (t0) REVERT: B 291 THR cc_start: 0.8603 (m) cc_final: 0.8397 (p) REVERT: B 454 ASN cc_start: 0.9006 (m-40) cc_final: 0.8569 (p0) REVERT: B 457 ASN cc_start: 0.8022 (m-40) cc_final: 0.7813 (m-40) REVERT: B 599 ASP cc_start: 0.7973 (m-30) cc_final: 0.7736 (m-30) REVERT: B 600 SER cc_start: 0.7758 (m) cc_final: 0.7536 (p) REVERT: B 941 LYS cc_start: 0.2532 (tttp) cc_final: 0.1716 (tttm) REVERT: B 986 VAL cc_start: 0.8809 (t) cc_final: 0.8544 (t) REVERT: B 1020 TRP cc_start: 0.8774 (m100) cc_final: 0.7913 (m100) REVERT: B 1136 LYS cc_start: 0.8260 (tppt) cc_final: 0.8048 (tppt) REVERT: B 1192 MET cc_start: 0.8114 (mmt) cc_final: 0.7760 (mmm) REVERT: B 1245 ILE cc_start: 0.8254 (mt) cc_final: 0.8040 (pt) REVERT: B 1293 LYS cc_start: 0.7998 (pttt) cc_final: 0.7680 (ptpt) REVERT: B 1294 ILE cc_start: 0.8629 (mt) cc_final: 0.8278 (pt) REVERT: B 1296 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7653 (tp30) REVERT: B 1300 VAL cc_start: 0.8687 (t) cc_final: 0.8241 (m) REVERT: B 1306 ASN cc_start: 0.8549 (m-40) cc_final: 0.8312 (m-40) REVERT: B 1334 ASP cc_start: 0.8039 (t0) cc_final: 0.7788 (t0) REVERT: B 1354 VAL cc_start: 0.8091 (t) cc_final: 0.7640 (p) REVERT: B 1356 VAL cc_start: 0.8441 (t) cc_final: 0.8148 (p) REVERT: C 129 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7479 (tm-30) REVERT: C 196 GLN cc_start: 0.9027 (mt0) cc_final: 0.8806 (mp10) REVERT: C 206 LYS cc_start: 0.9448 (mttm) cc_final: 0.9237 (ptpp) REVERT: C 212 LEU cc_start: 0.9175 (tp) cc_final: 0.8911 (mm) REVERT: C 229 TYR cc_start: 0.8710 (t80) cc_final: 0.8432 (t80) REVERT: C 247 LEU cc_start: 0.8495 (tp) cc_final: 0.8181 (tp) REVERT: C 268 ASN cc_start: 0.8803 (p0) cc_final: 0.8571 (p0) REVERT: C 301 ASN cc_start: 0.8581 (m-40) cc_final: 0.8253 (m-40) REVERT: C 307 TRP cc_start: 0.7869 (m100) cc_final: 0.7557 (m100) REVERT: C 314 LEU cc_start: 0.8854 (tp) cc_final: 0.8402 (mp) REVERT: C 324 LYS cc_start: 0.8858 (tttm) cc_final: 0.8619 (tptt) REVERT: C 369 MET cc_start: 0.8886 (mtm) cc_final: 0.8501 (mtm) REVERT: C 405 ASP cc_start: 0.5252 (t0) cc_final: 0.5020 (t0) REVERT: C 432 MET cc_start: 0.9007 (ttp) cc_final: 0.8792 (ttp) REVERT: C 433 LEU cc_start: 0.9048 (mt) cc_final: 0.8748 (tp) REVERT: D 67 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7182 (m-80) REVERT: D 114 MET cc_start: 0.8105 (mtp) cc_final: 0.7842 (mtm) REVERT: D 151 LEU cc_start: 0.8936 (mt) cc_final: 0.8664 (tp) REVERT: D 156 GLN cc_start: 0.8333 (mt0) cc_final: 0.7897 (pt0) REVERT: D 158 HIS cc_start: 0.7933 (m170) cc_final: 0.7204 (m170) REVERT: D 322 ASP cc_start: 0.8342 (t0) cc_final: 0.8027 (t0) REVERT: D 330 CYS cc_start: 0.8569 (t) cc_final: 0.7882 (t) REVERT: D 333 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7763 (mp0) REVERT: D 349 LYS cc_start: 0.9194 (mttt) cc_final: 0.8868 (mttt) REVERT: D 356 LEU cc_start: 0.8612 (mt) cc_final: 0.8386 (mm) REVERT: D 359 CYS cc_start: 0.8372 (m) cc_final: 0.7902 (t) REVERT: D 378 LEU cc_start: 0.8918 (tp) cc_final: 0.8649 (tt) REVERT: E 9 ASP cc_start: 0.7617 (p0) cc_final: 0.7005 (p0) REVERT: E 48 PHE cc_start: 0.8597 (p90) cc_final: 0.8236 (p90) REVERT: E 105 TRP cc_start: 0.8858 (m100) cc_final: 0.8402 (m100) REVERT: E 122 VAL cc_start: 0.8644 (t) cc_final: 0.8411 (p) REVERT: L -3 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8306 (mm-40) REVERT: L 17 ARG cc_start: 0.8445 (tpt-90) cc_final: 0.8146 (ttt-90) REVERT: L 32 SER cc_start: 0.8335 (m) cc_final: 0.7939 (p) REVERT: L 62 ASP cc_start: 0.8158 (m-30) cc_final: 0.7940 (m-30) REVERT: L 72 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8678 (tp-100) outliers start: 4 outliers final: 2 residues processed: 758 average time/residue: 0.2160 time to fit residues: 237.7854 Evaluate side-chains 561 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 558 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain I residue 21 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN A 186 HIS B 4 GLN B 12 GLN B 45 HIS B 295 HIS B 709 GLN B 746 HIS B 956 ASN B 988 HIS B 990 HIS B1055 HIS C 271 ASN D 169 ASN ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN D 363 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065498 restraints weight = 68834.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067415 restraints weight = 36131.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068661 restraints weight = 23892.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.069461 restraints weight = 18252.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069961 restraints weight = 15384.689| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24358 Z= 0.170 Angle : 0.659 15.690 32904 Z= 0.330 Chirality : 0.043 0.227 3644 Planarity : 0.005 0.108 4213 Dihedral : 7.162 154.210 3242 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 2.39 % Allowed : 15.98 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2920 helix: 0.58 (0.14), residues: 1351 sheet: 0.55 (0.29), residues: 315 loop : -1.48 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 115 TYR 0.016 0.002 TYR B 105 PHE 0.024 0.002 PHE E 31 TRP 0.023 0.002 TRP C 277 HIS 0.009 0.001 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (24349) covalent geometry : angle 0.63584 / 0.33 (32892) hydrogen bonds : bond 0.06122 / 4.04 ( 1050) hydrogen bonds : angle 4.46540 / 3.05 ( 3036) metal coordination : bond 0.01003 / 0.64 ( 8) metal coordination : angle 9.03815 / 4.83 ( 12) Misc. bond : bond 0.00357 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 586 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8377 (p) cc_final: 0.7995 (t) REVERT: A 27 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: A 187 MET cc_start: 0.8732 (ttm) cc_final: 0.8381 (ttm) REVERT: A 194 ASP cc_start: 0.7615 (m-30) cc_final: 0.7248 (m-30) REVERT: A 218 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.6865 (mtm) REVERT: A 262 MET cc_start: 0.8406 (mmt) cc_final: 0.7819 (mmt) REVERT: A 372 THR cc_start: 0.8355 (p) cc_final: 0.8078 (t) REVERT: A 486 ASN cc_start: 0.8079 (t0) cc_final: 0.7583 (t0) REVERT: A 498 ILE cc_start: 0.7623 (mm) cc_final: 0.6982 (tt) REVERT: A 516 MET cc_start: 0.8303 (tmm) cc_final: 0.7435 (tmm) REVERT: A 560 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7168 (mm-40) REVERT: A 636 LYS cc_start: 0.8130 (mttt) cc_final: 0.7821 (mtpt) REVERT: A 660 LYS cc_start: 0.8587 (tppt) cc_final: 0.8290 (tppt) REVERT: A 676 SER cc_start: 0.8653 (t) cc_final: 0.8341 (p) REVERT: A 678 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7960 (mmmm) REVERT: A 688 VAL cc_start: 0.8685 (t) cc_final: 0.8365 (p) REVERT: A 795 TYR cc_start: 0.7552 (t80) cc_final: 0.7242 (t80) REVERT: A 830 ASP cc_start: 0.7652 (m-30) cc_final: 0.7356 (m-30) REVERT: A 836 ASP cc_start: 0.7716 (p0) cc_final: 0.7360 (p0) REVERT: A 849 ASP cc_start: 0.7793 (p0) cc_final: 0.7518 (p0) REVERT: A 859 MET cc_start: 0.7876 (tpp) cc_final: 0.7555 (tpp) REVERT: B 288 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 941 LYS cc_start: 0.2236 (tttp) cc_final: 0.1509 (ttpp) REVERT: B 945 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 1140 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8614 (mmtm) REVERT: B 1192 MET cc_start: 0.8068 (mmt) cc_final: 0.7331 (mmt) REVERT: B 1276 SER cc_start: 0.8438 (m) cc_final: 0.7824 (p) REVERT: B 1290 TYR cc_start: 0.7127 (m-80) cc_final: 0.6596 (m-80) REVERT: B 1292 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7675 (ttp80) REVERT: B 1300 VAL cc_start: 0.8532 (t) cc_final: 0.8126 (m) REVERT: B 1334 ASP cc_start: 0.7648 (t0) cc_final: 0.7430 (t0) REVERT: B 1356 VAL cc_start: 0.8324 (t) cc_final: 0.8122 (m) REVERT: C 129 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7232 (tm-30) REVERT: C 181 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8433 (tm-30) REVERT: C 224 GLN cc_start: 0.9165 (mm110) cc_final: 0.8878 (mm-40) REVERT: C 229 TYR cc_start: 0.8343 (t80) cc_final: 0.8141 (t80) REVERT: C 247 LEU cc_start: 0.8421 (tp) cc_final: 0.8153 (tp) REVERT: C 263 LYS cc_start: 0.7399 (pptt) cc_final: 0.6956 (pptt) REVERT: C 300 TRP cc_start: 0.6315 (m100) cc_final: 0.5642 (m100) REVERT: C 301 ASN cc_start: 0.8269 (m-40) cc_final: 0.8046 (m110) REVERT: C 307 TRP cc_start: 0.7216 (m100) cc_final: 0.6996 (m100) REVERT: C 369 MET cc_start: 0.8594 (mtm) cc_final: 0.8072 (ppp) REVERT: C 433 LEU cc_start: 0.8972 (mt) cc_final: 0.8762 (pp) REVERT: D 145 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8522 (ptpp) REVERT: D 322 ASP cc_start: 0.7875 (t0) cc_final: 0.7656 (t0) REVERT: D 323 VAL cc_start: 0.8673 (t) cc_final: 0.8297 (m) REVERT: D 330 CYS cc_start: 0.8253 (t) cc_final: 0.7273 (t) REVERT: D 337 GLU cc_start: 0.7222 (pm20) cc_final: 0.6871 (pm20) REVERT: D 346 ARG cc_start: 0.8273 (mmm160) cc_final: 0.8000 (mmm160) REVERT: D 349 LYS cc_start: 0.9043 (mttt) cc_final: 0.8817 (mtpp) REVERT: D 378 LEU cc_start: 0.8961 (tp) cc_final: 0.8674 (tt) REVERT: E 9 ASP cc_start: 0.7000 (p0) cc_final: 0.6515 (p0) REVERT: E 89 VAL cc_start: 0.8295 (t) cc_final: 0.7921 (t) REVERT: E 105 TRP cc_start: 0.8711 (m100) cc_final: 0.8151 (m100) REVERT: E 122 VAL cc_start: 0.8666 (t) cc_final: 0.8462 (p) REVERT: E 144 ASP cc_start: 0.8560 (m-30) cc_final: 0.8336 (m-30) REVERT: L 17 ARG cc_start: 0.8431 (tpt-90) cc_final: 0.8222 (ttt-90) REVERT: L 29 GLU cc_start: 0.6391 (mp0) cc_final: 0.6182 (mp0) REVERT: L 58 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7319 (tm-30) REVERT: L 70 LEU cc_start: 0.8923 (tp) cc_final: 0.8602 (tp) REVERT: L 76 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7750 (pttm) REVERT: L 83 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8184 (ttp80) outliers start: 63 outliers final: 44 residues processed: 619 average time/residue: 0.1990 time to fit residues: 183.2179 Evaluate side-chains 566 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 520 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1351 ASP Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 23 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 196 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 218 optimal weight: 0.2980 chunk 150 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS A 560 GLN B 295 HIS C 179 GLN C 271 ASN D 319 HIS D 362 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064808 restraints weight = 68555.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066711 restraints weight = 36022.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067937 restraints weight = 23807.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068733 restraints weight = 18248.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069244 restraints weight = 15386.796| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24358 Z= 0.154 Angle : 0.620 11.513 32904 Z= 0.316 Chirality : 0.042 0.226 3644 Planarity : 0.005 0.107 4213 Dihedral : 7.110 155.379 3241 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 3.34 % Allowed : 17.54 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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 (0.15), residues: 2920 helix: 1.11 (0.14), residues: 1351 sheet: 0.58 (0.29), residues: 324 loop : -1.37 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 811 TYR 0.023 0.002 TYR C 394 PHE 0.019 0.002 PHE C 288 TRP 0.032 0.002 TRP C 277 HIS 0.006 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (24349) covalent geometry : angle 0.60983 / 0.32 (32892) hydrogen bonds : bond 0.05546 / 3.67 ( 1050) hydrogen bonds : angle 4.26010 / 2.93 ( 3036) metal coordination : bond 0.00704 / 0.43 ( 8) metal coordination : angle 5.97423 / 3.19 ( 12) Misc. bond : bond 0.00044 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 546 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8369 (p) cc_final: 0.7887 (t) REVERT: A 187 MET cc_start: 0.8737 (ttm) cc_final: 0.8453 (ttm) REVERT: A 194 ASP cc_start: 0.7681 (m-30) cc_final: 0.7261 (m-30) REVERT: A 218 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.6691 (mtm) REVERT: A 262 MET cc_start: 0.8416 (mmt) cc_final: 0.7828 (mmt) REVERT: A 372 THR cc_start: 0.8369 (p) cc_final: 0.8086 (t) REVERT: A 486 ASN cc_start: 0.8020 (t0) cc_final: 0.7474 (t0) REVERT: A 498 ILE cc_start: 0.7522 (mm) cc_final: 0.7072 (tt) REVERT: A 504 GLN cc_start: 0.7561 (mp10) cc_final: 0.7349 (mp10) REVERT: A 516 MET cc_start: 0.8287 (tmm) cc_final: 0.7360 (tmm) REVERT: A 560 GLN cc_start: 0.7672 (mm110) cc_final: 0.7282 (mm110) REVERT: A 576 LEU cc_start: 0.8331 (tp) cc_final: 0.8085 (tp) REVERT: A 596 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6641 (tm-30) REVERT: A 620 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 622 PHE cc_start: 0.8108 (m-80) cc_final: 0.7864 (m-80) REVERT: A 636 LYS cc_start: 0.8242 (mttt) cc_final: 0.7614 (mtpp) REVERT: A 676 SER cc_start: 0.8630 (t) cc_final: 0.8296 (p) REVERT: A 678 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8000 (mmmm) REVERT: A 688 VAL cc_start: 0.8664 (t) cc_final: 0.8323 (p) REVERT: A 796 GLN cc_start: 0.7291 (mp10) cc_final: 0.7005 (mp10) REVERT: A 830 ASP cc_start: 0.7716 (m-30) cc_final: 0.7393 (m-30) REVERT: A 836 ASP cc_start: 0.7735 (p0) cc_final: 0.7368 (p0) REVERT: A 844 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 849 ASP cc_start: 0.7827 (p0) cc_final: 0.7608 (p0) REVERT: A 859 MET cc_start: 0.8061 (tpp) cc_final: 0.7834 (tpp) REVERT: B 39 LYS cc_start: 0.8308 (mttt) cc_final: 0.8103 (mttp) REVERT: B 295 HIS cc_start: 0.7754 (t-90) cc_final: 0.6921 (t-170) REVERT: B 626 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8177 (m-30) REVERT: B 945 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: B 1020 TRP cc_start: 0.8656 (m100) cc_final: 0.7714 (m100) REVERT: B 1111 VAL cc_start: 0.8801 (t) cc_final: 0.8587 (m) REVERT: B 1136 LYS cc_start: 0.7773 (tppt) cc_final: 0.7570 (tppt) REVERT: B 1140 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8620 (mmtm) REVERT: B 1184 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8297 (ttm110) REVERT: B 1276 SER cc_start: 0.8367 (m) cc_final: 0.7763 (p) REVERT: B 1290 TYR cc_start: 0.7229 (m-80) cc_final: 0.6565 (m-80) REVERT: B 1296 GLU cc_start: 0.7247 (tp30) cc_final: 0.7037 (tp30) REVERT: B 1300 VAL cc_start: 0.8517 (t) cc_final: 0.8093 (m) REVERT: B 1330 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: C 129 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7213 (tm-30) REVERT: C 224 GLN cc_start: 0.9154 (mm110) cc_final: 0.8879 (mm-40) REVERT: C 245 ASP cc_start: 0.7453 (t70) cc_final: 0.7089 (t70) REVERT: C 247 LEU cc_start: 0.8379 (tp) cc_final: 0.8096 (tp) REVERT: C 263 LYS cc_start: 0.7465 (pptt) cc_final: 0.7142 (pptt) REVERT: C 271 ASN cc_start: 0.8105 (t0) cc_final: 0.7486 (t0) REVERT: C 277 TRP cc_start: 0.8022 (t60) cc_final: 0.7711 (t60) REVERT: C 285 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7612 (mm) REVERT: C 301 ASN cc_start: 0.8372 (m-40) cc_final: 0.8086 (m110) REVERT: C 307 TRP cc_start: 0.7300 (m100) cc_final: 0.7083 (m100) REVERT: C 317 LEU cc_start: 0.8497 (mt) cc_final: 0.8234 (pp) REVERT: C 330 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 369 MET cc_start: 0.8602 (mtm) cc_final: 0.8070 (ppp) REVERT: C 433 LEU cc_start: 0.9027 (mt) cc_final: 0.8746 (tp) REVERT: D 94 LYS cc_start: 0.8164 (pttp) cc_final: 0.7935 (pttm) REVERT: D 145 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8572 (ptpp) REVERT: D 322 ASP cc_start: 0.7924 (t0) cc_final: 0.7709 (t0) REVERT: D 323 VAL cc_start: 0.8695 (t) cc_final: 0.8315 (m) REVERT: D 327 LYS cc_start: 0.8822 (mttm) cc_final: 0.8591 (mtmm) REVERT: D 330 CYS cc_start: 0.8076 (t) cc_final: 0.7268 (t) REVERT: D 333 GLU cc_start: 0.7733 (mp0) cc_final: 0.7371 (mp0) REVERT: D 337 GLU cc_start: 0.7352 (pm20) cc_final: 0.6917 (pm20) REVERT: D 350 LYS cc_start: 0.7900 (mttt) cc_final: 0.7503 (mttt) REVERT: D 359 CYS cc_start: 0.7917 (m) cc_final: 0.7519 (p) REVERT: D 378 LEU cc_start: 0.8945 (tp) cc_final: 0.8604 (tt) REVERT: E 9 ASP cc_start: 0.6846 (p0) cc_final: 0.6417 (p0) REVERT: E 48 PHE cc_start: 0.8470 (p90) cc_final: 0.8189 (p90) REVERT: E 89 VAL cc_start: 0.8323 (t) cc_final: 0.7927 (t) REVERT: E 105 TRP cc_start: 0.8678 (m100) cc_final: 0.7997 (m100) REVERT: E 122 VAL cc_start: 0.8669 (t) cc_final: 0.8390 (p) REVERT: E 140 LYS cc_start: 0.8669 (tptm) cc_final: 0.8364 (tptt) REVERT: E 144 ASP cc_start: 0.8642 (m-30) cc_final: 0.8319 (m-30) REVERT: L -3 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8345 (mm-40) REVERT: L 58 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7540 (tm-30) REVERT: L 70 LEU cc_start: 0.8831 (tp) cc_final: 0.8440 (tp) outliers start: 88 outliers final: 48 residues processed: 594 average time/residue: 0.1887 time to fit residues: 166.7980 Evaluate side-chains 577 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 522 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 945 GLN Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1351 ASP Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 62 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 233 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 169 ASN D 319 HIS ** D 373 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 = 0.3357 r_free = 0.3357 target = 0.080060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064627 restraints weight = 68706.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066510 restraints weight = 35893.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.067732 restraints weight = 23740.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068520 restraints weight = 18209.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069034 restraints weight = 15358.643| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24358 Z= 0.150 Angle : 0.614 10.602 32904 Z= 0.312 Chirality : 0.042 0.228 3644 Planarity : 0.005 0.106 4213 Dihedral : 6.978 155.872 3239 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.42 % Allowed : 18.94 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: 0.22 (0.15), residues: 2920 helix: 1.36 (0.14), residues: 1341 sheet: 0.58 (0.29), residues: 324 loop : -1.35 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 811 TYR 0.018 0.001 TYR C 394 PHE 0.028 0.001 PHE C 274 TRP 0.018 0.001 TRP C 277 HIS 0.006 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (24349) covalent geometry : angle 0.60520 / 0.31 (32892) hydrogen bonds : bond 0.05299 / 3.53 ( 1050) hydrogen bonds : angle 4.15397 / 2.87 ( 3036) metal coordination : bond 0.00570 / 0.35 ( 8) metal coordination : angle 5.55792 / 2.98 ( 12) Misc. bond : bond 0.00044 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 545 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8357 (p) cc_final: 0.7909 (t) REVERT: A 27 GLU cc_start: 0.7470 (pt0) cc_final: 0.6900 (pm20) REVERT: A 187 MET cc_start: 0.8733 (ttm) cc_final: 0.8443 (ttm) REVERT: A 218 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6252 (mtm) REVERT: A 262 MET cc_start: 0.8440 (mmt) cc_final: 0.7891 (mmt) REVERT: A 344 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6605 (mm-30) REVERT: A 372 THR cc_start: 0.8365 (p) cc_final: 0.8081 (t) REVERT: A 486 ASN cc_start: 0.7948 (t0) cc_final: 0.7390 (t0) REVERT: A 498 ILE cc_start: 0.7697 (mm) cc_final: 0.7099 (tt) REVERT: A 516 MET cc_start: 0.8254 (tmm) cc_final: 0.7342 (tmm) REVERT: A 560 GLN cc_start: 0.7714 (mm110) cc_final: 0.7450 (mm110) REVERT: A 596 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 620 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 622 PHE cc_start: 0.8072 (m-80) cc_final: 0.7609 (m-80) REVERT: A 636 LYS cc_start: 0.8192 (mttt) cc_final: 0.7925 (mtpt) REVERT: A 687 SER cc_start: 0.8784 (p) cc_final: 0.8557 (p) REVERT: A 688 VAL cc_start: 0.8658 (t) cc_final: 0.8178 (p) REVERT: A 796 GLN cc_start: 0.7307 (mp10) cc_final: 0.6843 (mp10) REVERT: A 830 ASP cc_start: 0.7721 (m-30) cc_final: 0.7397 (m-30) REVERT: A 836 ASP cc_start: 0.7738 (p0) cc_final: 0.7376 (p0) REVERT: A 849 ASP cc_start: 0.7837 (p0) cc_final: 0.7620 (p0) REVERT: B 39 LYS cc_start: 0.8318 (mttt) cc_final: 0.8087 (mttp) REVERT: B 295 HIS cc_start: 0.7767 (t-90) cc_final: 0.7468 (t-170) REVERT: B 626 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: B 1020 TRP cc_start: 0.8645 (m100) cc_final: 0.7718 (m100) REVERT: B 1111 VAL cc_start: 0.8802 (t) cc_final: 0.8582 (m) REVERT: B 1136 LYS cc_start: 0.7783 (tppt) cc_final: 0.7544 (tppt) REVERT: B 1184 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8296 (ttm110) REVERT: B 1276 SER cc_start: 0.8344 (m) cc_final: 0.7653 (p) REVERT: B 1290 TYR cc_start: 0.7196 (m-80) cc_final: 0.6597 (m-80) REVERT: B 1292 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7680 (ttp80) REVERT: B 1300 VAL cc_start: 0.8500 (t) cc_final: 0.8089 (m) REVERT: B 1330 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: C 129 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7156 (tm-30) REVERT: C 206 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8979 (mtmt) REVERT: C 233 TYR cc_start: 0.8848 (t80) cc_final: 0.8600 (t80) REVERT: C 242 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7444 (mp0) REVERT: C 245 ASP cc_start: 0.7400 (t70) cc_final: 0.6985 (t70) REVERT: C 247 LEU cc_start: 0.8381 (tp) cc_final: 0.8096 (tp) REVERT: C 263 LYS cc_start: 0.7554 (pptt) cc_final: 0.7253 (pptt) REVERT: C 285 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7633 (mm) REVERT: C 301 ASN cc_start: 0.8346 (m-40) cc_final: 0.8042 (m110) REVERT: C 317 LEU cc_start: 0.8529 (mt) cc_final: 0.8249 (pp) REVERT: C 433 LEU cc_start: 0.8989 (mt) cc_final: 0.8773 (tp) REVERT: D 273 ASN cc_start: 0.7049 (p0) cc_final: 0.6771 (p0) REVERT: D 322 ASP cc_start: 0.7901 (t0) cc_final: 0.7680 (t0) REVERT: D 323 VAL cc_start: 0.8690 (t) cc_final: 0.8296 (m) REVERT: D 330 CYS cc_start: 0.8112 (t) cc_final: 0.7230 (t) REVERT: D 333 GLU cc_start: 0.7778 (mp0) cc_final: 0.7377 (mp0) REVERT: D 337 GLU cc_start: 0.7319 (pm20) cc_final: 0.6959 (pm20) REVERT: D 359 CYS cc_start: 0.7861 (m) cc_final: 0.7551 (p) REVERT: D 376 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5848 (ttp-110) REVERT: D 378 LEU cc_start: 0.8957 (tp) cc_final: 0.8626 (tt) REVERT: E 9 ASP cc_start: 0.6797 (p0) cc_final: 0.6394 (p0) REVERT: E 38 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7705 (mm-30) REVERT: E 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7756 (t80) REVERT: E 48 PHE cc_start: 0.8466 (p90) cc_final: 0.8180 (p90) REVERT: E 89 VAL cc_start: 0.8372 (t) cc_final: 0.7980 (t) REVERT: E 105 TRP cc_start: 0.8686 (m100) cc_final: 0.8205 (m100) REVERT: E 112 TYR cc_start: 0.8133 (m-80) cc_final: 0.7919 (m-10) REVERT: E 122 VAL cc_start: 0.8706 (t) cc_final: 0.8447 (p) REVERT: E 140 LYS cc_start: 0.8653 (tptm) cc_final: 0.8353 (tptt) REVERT: E 144 ASP cc_start: 0.8625 (m-30) cc_final: 0.8249 (m-30) REVERT: L 58 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7527 (tm-30) outliers start: 90 outliers final: 59 residues processed: 596 average time/residue: 0.1913 time to fit residues: 171.1134 Evaluate side-chains 586 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 522 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 62 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C 275 HIS D 169 ASN ** D 373 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 = 0.3344 r_free = 0.3344 target = 0.079359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063976 restraints weight = 68633.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065848 restraints weight = 35855.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067059 restraints weight = 23726.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067836 restraints weight = 18238.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068265 restraints weight = 15418.674| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24358 Z= 0.163 Angle : 0.622 9.935 32904 Z= 0.316 Chirality : 0.043 0.227 3644 Planarity : 0.005 0.106 4213 Dihedral : 6.986 155.630 3239 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.26 % Allowed : 19.36 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2920 helix: 1.42 (0.15), residues: 1347 sheet: 0.49 (0.29), residues: 328 loop : -1.35 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1040 TYR 0.023 0.002 TYR C 394 PHE 0.017 0.002 PHE C 274 TRP 0.021 0.002 TRP C 277 HIS 0.017 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (24349) covalent geometry : angle 0.61372 / 0.32 (32892) hydrogen bonds : bond 0.05416 / 3.61 ( 1050) hydrogen bonds : angle 4.12974 / 2.86 ( 3036) metal coordination : bond 0.00539 / 0.33 ( 8) metal coordination : angle 5.25337 / 2.82 ( 12) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 530 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8346 (p) cc_final: 0.7917 (t) REVERT: A 27 GLU cc_start: 0.7448 (pt0) cc_final: 0.6889 (pm20) REVERT: A 187 MET cc_start: 0.8749 (ttm) cc_final: 0.8460 (ttm) REVERT: A 218 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6166 (mtm) REVERT: A 262 MET cc_start: 0.8432 (mmt) cc_final: 0.7850 (mmt) REVERT: A 350 GLU cc_start: 0.7443 (pp20) cc_final: 0.7173 (pp20) REVERT: A 372 THR cc_start: 0.8367 (p) cc_final: 0.8108 (t) REVERT: A 472 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5863 (pm20) REVERT: A 486 ASN cc_start: 0.7909 (t0) cc_final: 0.7372 (t0) REVERT: A 516 MET cc_start: 0.8243 (tmm) cc_final: 0.7403 (tmm) REVERT: A 561 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: A 596 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 620 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 622 PHE cc_start: 0.8076 (m-80) cc_final: 0.7609 (m-80) REVERT: A 636 LYS cc_start: 0.8206 (mttt) cc_final: 0.7932 (mtpt) REVERT: A 639 ASP cc_start: 0.7691 (p0) cc_final: 0.7435 (p0) REVERT: A 640 ASP cc_start: 0.7829 (m-30) cc_final: 0.7546 (m-30) REVERT: A 678 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7995 (mmmm) REVERT: A 687 SER cc_start: 0.8780 (p) cc_final: 0.8503 (p) REVERT: A 688 VAL cc_start: 0.8656 (t) cc_final: 0.8193 (p) REVERT: A 796 GLN cc_start: 0.7364 (mp10) cc_final: 0.6818 (mp10) REVERT: A 830 ASP cc_start: 0.7726 (m-30) cc_final: 0.7414 (m-30) REVERT: A 836 ASP cc_start: 0.7740 (p0) cc_final: 0.7391 (p0) REVERT: A 844 ASP cc_start: 0.7729 (t0) cc_final: 0.7483 (t0) REVERT: A 849 ASP cc_start: 0.7860 (p0) cc_final: 0.7585 (p0) REVERT: B 39 LYS cc_start: 0.8322 (mttt) cc_final: 0.8104 (mttp) REVERT: B 275 GLU cc_start: 0.7788 (pm20) cc_final: 0.7417 (tp30) REVERT: B 626 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: B 1019 ILE cc_start: 0.8434 (mp) cc_final: 0.8056 (pt) REVERT: B 1020 TRP cc_start: 0.8687 (m100) cc_final: 0.7704 (m100) REVERT: B 1136 LYS cc_start: 0.7817 (tppt) cc_final: 0.7564 (tppt) REVERT: B 1276 SER cc_start: 0.8350 (m) cc_final: 0.7632 (p) REVERT: B 1290 TYR cc_start: 0.7194 (m-80) cc_final: 0.6545 (m-80) REVERT: B 1292 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7701 (ttp80) REVERT: B 1330 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: C 129 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7139 (tm-30) REVERT: C 226 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: C 245 ASP cc_start: 0.7389 (t70) cc_final: 0.6911 (t70) REVERT: C 247 LEU cc_start: 0.8396 (tp) cc_final: 0.8116 (tp) REVERT: C 263 LYS cc_start: 0.7501 (pptt) cc_final: 0.7214 (pptt) REVERT: C 277 TRP cc_start: 0.8195 (t60) cc_final: 0.7814 (t60) REVERT: C 285 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7652 (mm) REVERT: C 317 LEU cc_start: 0.8509 (mt) cc_final: 0.8214 (pp) REVERT: C 369 MET cc_start: 0.8520 (mtm) cc_final: 0.8039 (ppp) REVERT: C 433 LEU cc_start: 0.8999 (mt) cc_final: 0.8721 (tp) REVERT: C 436 LEU cc_start: 0.8340 (mt) cc_final: 0.8011 (mt) REVERT: D 118 MET cc_start: 0.7657 (mmm) cc_final: 0.7175 (mtm) REVERT: D 273 ASN cc_start: 0.7007 (p0) cc_final: 0.6620 (p0) REVERT: D 322 ASP cc_start: 0.7915 (t0) cc_final: 0.7689 (t0) REVERT: D 323 VAL cc_start: 0.8653 (t) cc_final: 0.8280 (m) REVERT: D 330 CYS cc_start: 0.8125 (t) cc_final: 0.7469 (p) REVERT: D 359 CYS cc_start: 0.7882 (m) cc_final: 0.7609 (p) REVERT: D 376 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5715 (ttp-110) REVERT: D 378 LEU cc_start: 0.8971 (tp) cc_final: 0.8640 (tt) REVERT: E 9 ASP cc_start: 0.6797 (p0) cc_final: 0.6423 (p0) REVERT: E 38 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7700 (mm-30) REVERT: E 40 TYR cc_start: 0.8101 (t80) cc_final: 0.7774 (t80) REVERT: E 48 PHE cc_start: 0.8463 (p90) cc_final: 0.8138 (p90) REVERT: E 105 TRP cc_start: 0.8685 (m100) cc_final: 0.8235 (m100) REVERT: E 122 VAL cc_start: 0.8737 (t) cc_final: 0.8469 (p) REVERT: E 140 LYS cc_start: 0.8661 (tptm) cc_final: 0.8344 (tptt) REVERT: E 144 ASP cc_start: 0.8621 (m-30) cc_final: 0.8232 (m-30) REVERT: I 17 VAL cc_start: 0.7699 (t) cc_final: 0.7472 (p) REVERT: L 17 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7821 (ttt-90) REVERT: L 58 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7392 (tm-30) outliers start: 86 outliers final: 55 residues processed: 578 average time/residue: 0.1908 time to fit residues: 165.6825 Evaluate side-chains 568 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 505 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 62 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 263 optimal weight: 0.0470 chunk 217 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.0010 chunk 259 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 287 optimal weight: 0.1980 overall best weight: 0.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C 301 ASN C 319 ASN D 169 ASN D 319 HIS D 362 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.081321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065778 restraints weight = 68680.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067732 restraints weight = 35459.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068995 restraints weight = 23176.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069773 restraints weight = 17646.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070304 restraints weight = 14854.982| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 24358 Z= 0.112 Angle : 0.589 9.629 32904 Z= 0.296 Chirality : 0.040 0.232 3644 Planarity : 0.004 0.104 4213 Dihedral : 6.768 154.933 3239 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 2.96 % Allowed : 20.16 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2920 helix: 1.65 (0.15), residues: 1344 sheet: 0.48 (0.29), residues: 330 loop : -1.22 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1184 TYR 0.026 0.001 TYR C 229 PHE 0.021 0.001 PHE D 395 TRP 0.018 0.001 TRP C 277 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24349) covalent geometry : angle 0.58281 / 0.30 (32892) hydrogen bonds : bond 0.04301 / 2.90 ( 1050) hydrogen bonds : angle 3.86326 / 2.68 ( 3036) metal coordination : bond 0.00618 / 0.34 ( 8) metal coordination : angle 4.65053 / 2.53 ( 12) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 522 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8326 (p) cc_final: 0.7969 (t) REVERT: A 187 MET cc_start: 0.8719 (ttm) cc_final: 0.8426 (ttm) REVERT: A 344 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6593 (mm-30) REVERT: A 372 THR cc_start: 0.8343 (p) cc_final: 0.8100 (t) REVERT: A 385 ARG cc_start: 0.5502 (ttp-170) cc_final: 0.5112 (ptp-170) REVERT: A 472 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5422 (pm20) REVERT: A 486 ASN cc_start: 0.7775 (t0) cc_final: 0.7156 (t0) REVERT: A 516 MET cc_start: 0.8275 (tmm) cc_final: 0.7410 (tmm) REVERT: A 596 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6602 (tm-30) REVERT: A 620 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 622 PHE cc_start: 0.8052 (m-80) cc_final: 0.7599 (m-80) REVERT: A 636 LYS cc_start: 0.8160 (mttt) cc_final: 0.7889 (mtpt) REVERT: A 639 ASP cc_start: 0.7654 (p0) cc_final: 0.7409 (p0) REVERT: A 649 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: A 678 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8035 (mmmm) REVERT: A 687 SER cc_start: 0.8691 (p) cc_final: 0.8370 (t) REVERT: A 688 VAL cc_start: 0.8611 (t) cc_final: 0.8015 (p) REVERT: A 796 GLN cc_start: 0.7403 (mp10) cc_final: 0.6892 (mp10) REVERT: A 830 ASP cc_start: 0.7756 (m-30) cc_final: 0.7431 (m-30) REVERT: A 836 ASP cc_start: 0.7703 (p0) cc_final: 0.7350 (p0) REVERT: A 849 ASP cc_start: 0.7853 (p0) cc_final: 0.7579 (p0) REVERT: B 495 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7825 (ttp-110) REVERT: B 941 LYS cc_start: 0.2682 (tttp) cc_final: 0.1535 (pttp) REVERT: B 945 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: B 1020 TRP cc_start: 0.8669 (m100) cc_final: 0.7685 (m100) REVERT: B 1022 SER cc_start: 0.8466 (m) cc_final: 0.8140 (p) REVERT: B 1097 CYS cc_start: 0.8204 (p) cc_final: 0.7963 (p) REVERT: B 1111 VAL cc_start: 0.8838 (t) cc_final: 0.8586 (m) REVERT: B 1136 LYS cc_start: 0.7742 (tppt) cc_final: 0.7473 (tppt) REVERT: B 1276 SER cc_start: 0.8291 (m) cc_final: 0.7581 (p) REVERT: B 1290 TYR cc_start: 0.7024 (m-80) cc_final: 0.6399 (m-80) REVERT: C 129 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7153 (tm-30) REVERT: C 226 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: C 245 ASP cc_start: 0.7460 (t70) cc_final: 0.7015 (t70) REVERT: C 247 LEU cc_start: 0.8367 (tp) cc_final: 0.8091 (tp) REVERT: C 263 LYS cc_start: 0.7549 (pptt) cc_final: 0.7308 (pptt) REVERT: C 277 TRP cc_start: 0.8230 (t60) cc_final: 0.7841 (t60) REVERT: C 285 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7627 (mm) REVERT: C 302 GLU cc_start: 0.7642 (tt0) cc_final: 0.6803 (tp30) REVERT: C 369 MET cc_start: 0.8453 (mtm) cc_final: 0.8014 (ppp) REVERT: C 432 MET cc_start: 0.8813 (ttp) cc_final: 0.8522 (ptp) REVERT: C 433 LEU cc_start: 0.8988 (mt) cc_final: 0.8735 (tp) REVERT: C 436 LEU cc_start: 0.8377 (mt) cc_final: 0.8076 (mt) REVERT: D 118 MET cc_start: 0.7479 (mmm) cc_final: 0.7146 (mtm) REVERT: D 273 ASN cc_start: 0.7113 (p0) cc_final: 0.6884 (p0) REVERT: D 322 ASP cc_start: 0.7914 (t0) cc_final: 0.7677 (t0) REVERT: D 327 LYS cc_start: 0.8700 (mttm) cc_final: 0.8488 (mtmm) REVERT: D 330 CYS cc_start: 0.8131 (t) cc_final: 0.7421 (p) REVERT: D 350 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7452 (mmtt) REVERT: D 359 CYS cc_start: 0.7810 (m) cc_final: 0.7540 (p) REVERT: D 378 LEU cc_start: 0.8902 (tp) cc_final: 0.8555 (tt) REVERT: E 9 ASP cc_start: 0.6778 (p0) cc_final: 0.6444 (p0) REVERT: E 38 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7660 (mm-30) REVERT: E 40 TYR cc_start: 0.8126 (t80) cc_final: 0.7820 (t80) REVERT: E 48 PHE cc_start: 0.8448 (p90) cc_final: 0.8135 (p90) REVERT: E 105 TRP cc_start: 0.8672 (m100) cc_final: 0.8275 (m100) REVERT: E 122 VAL cc_start: 0.8738 (t) cc_final: 0.8466 (m) REVERT: E 137 THR cc_start: 0.8318 (p) cc_final: 0.6198 (p) REVERT: E 140 LYS cc_start: 0.8619 (tptm) cc_final: 0.8306 (tptt) REVERT: E 144 ASP cc_start: 0.8619 (m-30) cc_final: 0.8250 (m-30) REVERT: L 35 LYS cc_start: 0.8362 (pttp) cc_final: 0.7953 (pttp) REVERT: L 51 GLU cc_start: 0.8139 (tp30) cc_final: 0.7933 (mm-30) REVERT: L 58 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7493 (tm-30) REVERT: L 77 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7790 (tmm160) REVERT: L 80 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8480 (tmm160) outliers start: 78 outliers final: 54 residues processed: 567 average time/residue: 0.1796 time to fit residues: 151.8686 Evaluate side-chains 558 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 499 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 945 GLN Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1046 LYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 149 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C 319 ASN D 169 ASN D 362 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064032 restraints weight = 68813.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065904 restraints weight = 35851.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067106 restraints weight = 23692.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067881 restraints weight = 18234.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068364 restraints weight = 15411.613| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24358 Z= 0.171 Angle : 0.636 9.543 32904 Z= 0.322 Chirality : 0.043 0.231 3644 Planarity : 0.005 0.104 4213 Dihedral : 6.895 155.309 3239 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 3.26 % Allowed : 20.27 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2920 helix: 1.54 (0.15), residues: 1349 sheet: 0.48 (0.29), residues: 327 loop : -1.29 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 376 TYR 0.034 0.002 TYR C 229 PHE 0.021 0.002 PHE D 395 TRP 0.014 0.002 TRP C 277 HIS 0.021 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (24349) covalent geometry : angle 0.62855 / 0.32 (32892) hydrogen bonds : bond 0.05248 / 3.50 ( 1050) hydrogen bonds : angle 4.02616 / 2.79 ( 3036) metal coordination : bond 0.00565 / 0.36 ( 8) metal coordination : angle 5.22885 / 2.85 ( 12) Misc. bond : bond 0.00058 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 502 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8750 (ttm) cc_final: 0.8446 (ttm) REVERT: A 344 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6651 (mm-30) REVERT: A 347 GLN cc_start: 0.8368 (tp40) cc_final: 0.8095 (tp40) REVERT: A 372 THR cc_start: 0.8369 (p) cc_final: 0.8119 (t) REVERT: A 385 ARG cc_start: 0.5485 (ttp-170) cc_final: 0.5118 (ptp-170) REVERT: A 472 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5717 (pm20) REVERT: A 486 ASN cc_start: 0.7830 (t0) cc_final: 0.7294 (t0) REVERT: A 516 MET cc_start: 0.8257 (tmm) cc_final: 0.7364 (tmm) REVERT: A 561 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7462 (mtm-85) REVERT: A 620 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 622 PHE cc_start: 0.8105 (m-80) cc_final: 0.7680 (m-80) REVERT: A 636 LYS cc_start: 0.8217 (mttt) cc_final: 0.7970 (mtpt) REVERT: A 639 ASP cc_start: 0.7661 (p0) cc_final: 0.7403 (p0) REVERT: A 640 ASP cc_start: 0.7865 (m-30) cc_final: 0.7562 (m-30) REVERT: A 649 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: A 678 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8073 (mmmm) REVERT: A 687 SER cc_start: 0.8753 (p) cc_final: 0.8471 (p) REVERT: A 688 VAL cc_start: 0.8685 (t) cc_final: 0.8241 (p) REVERT: A 796 GLN cc_start: 0.7456 (mp10) cc_final: 0.6885 (mp10) REVERT: A 830 ASP cc_start: 0.7765 (m-30) cc_final: 0.7390 (m-30) REVERT: A 836 ASP cc_start: 0.7764 (p0) cc_final: 0.7430 (p0) REVERT: A 849 ASP cc_start: 0.7855 (p0) cc_final: 0.7593 (p0) REVERT: B 945 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: B 952 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7302 (mmt-90) REVERT: B 1020 TRP cc_start: 0.8683 (m100) cc_final: 0.7725 (m100) REVERT: B 1078 LYS cc_start: 0.7545 (tptp) cc_final: 0.7221 (tptt) REVERT: B 1111 VAL cc_start: 0.8846 (t) cc_final: 0.8602 (m) REVERT: B 1136 LYS cc_start: 0.7842 (tppt) cc_final: 0.7601 (tppt) REVERT: B 1276 SER cc_start: 0.8368 (m) cc_final: 0.7606 (p) REVERT: B 1290 TYR cc_start: 0.7125 (m-80) cc_final: 0.6486 (m-80) REVERT: B 1300 VAL cc_start: 0.8566 (t) cc_final: 0.8224 (m) REVERT: B 1330 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: C 129 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7134 (tm-30) REVERT: C 181 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 185 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7676 (tptm) REVERT: C 226 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: C 242 GLU cc_start: 0.7528 (mp0) cc_final: 0.7217 (mp0) REVERT: C 245 ASP cc_start: 0.7434 (t70) cc_final: 0.6916 (t70) REVERT: C 247 LEU cc_start: 0.8401 (tp) cc_final: 0.8118 (tp) REVERT: C 263 LYS cc_start: 0.7599 (pptt) cc_final: 0.7269 (pptt) REVERT: C 285 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7649 (mm) REVERT: C 302 GLU cc_start: 0.7651 (tt0) cc_final: 0.7410 (tt0) REVERT: C 369 MET cc_start: 0.8444 (mtm) cc_final: 0.7992 (ppp) REVERT: C 433 LEU cc_start: 0.8969 (mt) cc_final: 0.8709 (tp) REVERT: C 436 LEU cc_start: 0.8386 (mt) cc_final: 0.8075 (mt) REVERT: D 118 MET cc_start: 0.7515 (mmm) cc_final: 0.7106 (mtm) REVERT: D 322 ASP cc_start: 0.7889 (t0) cc_final: 0.7582 (t0) REVERT: D 330 CYS cc_start: 0.8134 (t) cc_final: 0.7482 (p) REVERT: D 359 CYS cc_start: 0.7964 (m) cc_final: 0.7623 (p) REVERT: D 376 ARG cc_start: 0.6492 (ttp80) cc_final: 0.6281 (ttm110) REVERT: D 378 LEU cc_start: 0.8962 (tp) cc_final: 0.8617 (tt) REVERT: E 38 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 40 TYR cc_start: 0.8203 (t80) cc_final: 0.7818 (t80) REVERT: E 48 PHE cc_start: 0.8458 (p90) cc_final: 0.8120 (p90) REVERT: E 105 TRP cc_start: 0.8644 (m100) cc_final: 0.8224 (m100) REVERT: E 122 VAL cc_start: 0.8713 (t) cc_final: 0.8445 (m) REVERT: E 140 LYS cc_start: 0.8660 (tptm) cc_final: 0.8381 (tptt) REVERT: E 144 ASP cc_start: 0.8622 (m-30) cc_final: 0.8241 (m-30) REVERT: L 1 MET cc_start: 0.8994 (mtp) cc_final: 0.8766 (mtp) REVERT: L 17 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7826 (ttt-90) REVERT: L 58 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 86 outliers final: 62 residues processed: 551 average time/residue: 0.1851 time to fit residues: 152.4013 Evaluate side-chains 558 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 489 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 945 GLN Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1046 LYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 230 optimal weight: 0.0570 chunk 259 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN C 271 ASN D 89 GLN D 169 ASN L 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064529 restraints weight = 68666.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066415 restraints weight = 35869.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067631 restraints weight = 23718.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068415 restraints weight = 18232.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068920 restraints weight = 15387.059| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24358 Z= 0.137 Angle : 0.627 9.244 32904 Z= 0.316 Chirality : 0.042 0.259 3644 Planarity : 0.004 0.103 4213 Dihedral : 6.867 155.077 3239 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.52 % Favored : 95.34 % Rotamer: Outliers : 2.89 % Allowed : 20.84 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.43 (0.16), residues: 2920 helix: 1.63 (0.15), residues: 1340 sheet: 0.37 (0.28), residues: 328 loop : -1.26 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 170 TYR 0.038 0.001 TYR C 229 PHE 0.021 0.001 PHE D 395 TRP 0.013 0.001 TRP C 277 HIS 0.012 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (24349) covalent geometry : angle 0.62030 / 0.32 (32892) hydrogen bonds : bond 0.04911 / 3.29 ( 1050) hydrogen bonds : angle 3.94695 / 2.73 ( 3036) metal coordination : bond 0.00527 / 0.32 ( 8) metal coordination : angle 4.76241 / 2.59 ( 12) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 499 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8725 (ttm) cc_final: 0.8425 (ttm) REVERT: A 344 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6615 (mm-30) REVERT: A 347 GLN cc_start: 0.8341 (tp40) cc_final: 0.8086 (tp40) REVERT: A 372 THR cc_start: 0.8345 (p) cc_final: 0.8105 (t) REVERT: A 385 ARG cc_start: 0.5369 (ttp-170) cc_final: 0.5133 (ptp-170) REVERT: A 472 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5795 (pm20) REVERT: A 486 ASN cc_start: 0.7791 (t0) cc_final: 0.7201 (t0) REVERT: A 516 MET cc_start: 0.8250 (tmm) cc_final: 0.7401 (tmm) REVERT: A 560 GLN cc_start: 0.7421 (mm110) cc_final: 0.7150 (mm110) REVERT: A 561 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7502 (mtm-85) REVERT: A 601 ILE cc_start: 0.8349 (mt) cc_final: 0.8141 (tp) REVERT: A 620 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 622 PHE cc_start: 0.8043 (m-80) cc_final: 0.7679 (m-80) REVERT: A 636 LYS cc_start: 0.8217 (mttt) cc_final: 0.7950 (mtpt) REVERT: A 639 ASP cc_start: 0.7620 (p0) cc_final: 0.7396 (p0) REVERT: A 649 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: A 678 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8009 (mmmm) REVERT: A 687 SER cc_start: 0.8721 (p) cc_final: 0.8388 (t) REVERT: A 688 VAL cc_start: 0.8702 (t) cc_final: 0.8124 (p) REVERT: A 796 GLN cc_start: 0.7477 (mp10) cc_final: 0.6900 (mp10) REVERT: A 830 ASP cc_start: 0.7767 (m-30) cc_final: 0.7393 (m-30) REVERT: A 836 ASP cc_start: 0.7744 (p0) cc_final: 0.7405 (p0) REVERT: A 849 ASP cc_start: 0.7848 (p0) cc_final: 0.7556 (p0) REVERT: B 495 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7905 (ttp-110) REVERT: B 945 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: B 952 ARG cc_start: 0.7503 (mmt-90) cc_final: 0.7251 (mmt-90) REVERT: B 969 GLU cc_start: 0.7907 (mp0) cc_final: 0.7656 (mp0) REVERT: B 1020 TRP cc_start: 0.8698 (m100) cc_final: 0.7713 (m100) REVERT: B 1136 LYS cc_start: 0.7796 (tppt) cc_final: 0.7584 (tppt) REVERT: B 1276 SER cc_start: 0.8335 (m) cc_final: 0.7612 (p) REVERT: B 1290 TYR cc_start: 0.7054 (m-80) cc_final: 0.6437 (m-80) REVERT: B 1300 VAL cc_start: 0.8533 (t) cc_final: 0.8189 (m) REVERT: C 129 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7115 (tm-30) REVERT: C 181 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 185 LYS cc_start: 0.8109 (tmtt) cc_final: 0.7658 (tptm) REVERT: C 242 GLU cc_start: 0.7525 (mp0) cc_final: 0.7251 (mp0) REVERT: C 245 ASP cc_start: 0.7454 (t70) cc_final: 0.6960 (t70) REVERT: C 247 LEU cc_start: 0.8391 (tp) cc_final: 0.8107 (tp) REVERT: C 263 LYS cc_start: 0.7573 (pptt) cc_final: 0.7307 (pptt) REVERT: C 285 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7631 (mm) REVERT: C 302 GLU cc_start: 0.7689 (tt0) cc_final: 0.6903 (tp30) REVERT: C 369 MET cc_start: 0.8365 (mtm) cc_final: 0.7975 (ppp) REVERT: C 433 LEU cc_start: 0.8985 (mt) cc_final: 0.8711 (tp) REVERT: C 436 LEU cc_start: 0.8386 (mt) cc_final: 0.8079 (mt) REVERT: D 118 MET cc_start: 0.7494 (mmm) cc_final: 0.7137 (mtm) REVERT: D 161 LYS cc_start: 0.8909 (tptt) cc_final: 0.8666 (tppt) REVERT: D 322 ASP cc_start: 0.7888 (t0) cc_final: 0.7609 (t0) REVERT: D 330 CYS cc_start: 0.8137 (t) cc_final: 0.7476 (p) REVERT: D 359 CYS cc_start: 0.7866 (m) cc_final: 0.7594 (p) REVERT: D 378 LEU cc_start: 0.8947 (tp) cc_final: 0.8607 (tt) REVERT: E 38 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7708 (mm-30) REVERT: E 40 TYR cc_start: 0.8194 (t80) cc_final: 0.7832 (t80) REVERT: E 48 PHE cc_start: 0.8461 (p90) cc_final: 0.8173 (p90) REVERT: E 105 TRP cc_start: 0.8610 (m100) cc_final: 0.8172 (m100) REVERT: E 122 VAL cc_start: 0.8726 (t) cc_final: 0.8479 (m) REVERT: E 140 LYS cc_start: 0.8668 (tptm) cc_final: 0.8432 (tptt) REVERT: E 144 ASP cc_start: 0.8593 (m-30) cc_final: 0.8273 (m-30) REVERT: L 1 MET cc_start: 0.8988 (mtp) cc_final: 0.8762 (mtp) REVERT: L 35 LYS cc_start: 0.8365 (pttp) cc_final: 0.7930 (pttp) REVERT: L 58 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7549 (tm-30) REVERT: L 76 LYS cc_start: 0.8415 (pttt) cc_final: 0.8094 (pttm) outliers start: 76 outliers final: 61 residues processed: 542 average time/residue: 0.1880 time to fit residues: 153.0301 Evaluate side-chains 557 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 492 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 945 GLN Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1046 LYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 215 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 284 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 290 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN D 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063519 restraints weight = 69474.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065426 restraints weight = 35521.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066653 restraints weight = 23243.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067439 restraints weight = 17751.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067928 restraints weight = 14948.752| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24358 Z= 0.165 Angle : 0.653 9.034 32904 Z= 0.330 Chirality : 0.043 0.230 3644 Planarity : 0.005 0.102 4213 Dihedral : 6.923 155.068 3239 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 2.81 % Allowed : 21.26 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: 0.35 (0.16), residues: 2920 helix: 1.54 (0.15), residues: 1346 sheet: 0.37 (0.28), residues: 327 loop : -1.29 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1292 TYR 0.043 0.002 TYR D 152 PHE 0.019 0.001 PHE D 395 TRP 0.020 0.002 TRP L 75 HIS 0.016 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (24349) covalent geometry : angle 0.64643 / 0.33 (32892) hydrogen bonds : bond 0.05304 / 3.56 ( 1050) hydrogen bonds : angle 4.05558 / 2.79 ( 3036) metal coordination : bond 0.00555 / 0.36 ( 8) metal coordination : angle 4.91201 / 2.68 ( 12) Misc. bond : bond 0.00045 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 513 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8714 (ttm) cc_final: 0.8412 (ttm) REVERT: A 344 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 347 GLN cc_start: 0.8334 (tp40) cc_final: 0.8111 (tp40) REVERT: A 372 THR cc_start: 0.8383 (p) cc_final: 0.8125 (t) REVERT: A 385 ARG cc_start: 0.5424 (ttp-170) cc_final: 0.5168 (ptp-170) REVERT: A 472 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: A 486 ASN cc_start: 0.7799 (t0) cc_final: 0.7293 (t0) REVERT: A 516 MET cc_start: 0.8240 (tmm) cc_final: 0.7358 (tmm) REVERT: A 561 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7643 (mtm-85) REVERT: A 620 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 622 PHE cc_start: 0.8026 (m-80) cc_final: 0.7639 (m-80) REVERT: A 636 LYS cc_start: 0.8216 (mttt) cc_final: 0.7981 (mtpt) REVERT: A 639 ASP cc_start: 0.7615 (p0) cc_final: 0.7340 (p0) REVERT: A 640 ASP cc_start: 0.7844 (m-30) cc_final: 0.7522 (m-30) REVERT: A 649 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 687 SER cc_start: 0.8726 (p) cc_final: 0.8425 (t) REVERT: A 688 VAL cc_start: 0.8721 (t) cc_final: 0.8153 (p) REVERT: A 796 GLN cc_start: 0.7519 (mp10) cc_final: 0.6936 (mp10) REVERT: A 830 ASP cc_start: 0.7758 (m-30) cc_final: 0.7382 (m-30) REVERT: A 836 ASP cc_start: 0.7717 (p0) cc_final: 0.7402 (p0) REVERT: A 849 ASP cc_start: 0.7787 (p0) cc_final: 0.7503 (p0) REVERT: B 558 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: B 626 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: B 941 LYS cc_start: 0.4193 (tttt) cc_final: 0.2441 (pttp) REVERT: B 952 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7264 (mmt-90) REVERT: B 969 GLU cc_start: 0.7966 (mp0) cc_final: 0.7733 (mp0) REVERT: B 1020 TRP cc_start: 0.8694 (m100) cc_final: 0.7761 (m100) REVERT: B 1078 LYS cc_start: 0.7552 (tptp) cc_final: 0.7322 (tptt) REVERT: B 1215 MET cc_start: 0.7085 (ttp) cc_final: 0.6883 (ttp) REVERT: B 1276 SER cc_start: 0.8347 (m) cc_final: 0.7587 (p) REVERT: B 1290 TYR cc_start: 0.7128 (m-80) cc_final: 0.6511 (m-80) REVERT: B 1292 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7777 (ttp80) REVERT: B 1300 VAL cc_start: 0.8537 (t) cc_final: 0.8192 (m) REVERT: B 1334 ASP cc_start: 0.7262 (t0) cc_final: 0.7027 (t0) REVERT: C 129 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7106 (tm-30) REVERT: C 181 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8564 (tm-30) REVERT: C 185 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7682 (tptm) REVERT: C 206 LYS cc_start: 0.9286 (mtmt) cc_final: 0.9074 (mttt) REVERT: C 242 GLU cc_start: 0.7511 (mp0) cc_final: 0.7280 (mp0) REVERT: C 245 ASP cc_start: 0.7400 (t70) cc_final: 0.6910 (t70) REVERT: C 247 LEU cc_start: 0.8395 (tp) cc_final: 0.8134 (tp) REVERT: C 285 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7695 (mm) REVERT: C 369 MET cc_start: 0.8318 (mtm) cc_final: 0.7954 (ppp) REVERT: C 433 LEU cc_start: 0.8964 (mt) cc_final: 0.8697 (tp) REVERT: C 436 LEU cc_start: 0.8384 (mt) cc_final: 0.8081 (mt) REVERT: D 118 MET cc_start: 0.7517 (mmm) cc_final: 0.7145 (mtm) REVERT: D 145 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8209 (pttm) REVERT: D 148 ASN cc_start: 0.8174 (m-40) cc_final: 0.7972 (m110) REVERT: D 154 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7748 (ttp80) REVERT: D 322 ASP cc_start: 0.7872 (t0) cc_final: 0.7572 (t0) REVERT: D 330 CYS cc_start: 0.8136 (t) cc_final: 0.7513 (p) REVERT: D 359 CYS cc_start: 0.7861 (m) cc_final: 0.7617 (p) REVERT: D 378 LEU cc_start: 0.8976 (tp) cc_final: 0.8620 (tt) REVERT: E 38 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 40 TYR cc_start: 0.8215 (t80) cc_final: 0.7848 (t80) REVERT: E 48 PHE cc_start: 0.8475 (p90) cc_final: 0.8204 (p90) REVERT: E 105 TRP cc_start: 0.8588 (m100) cc_final: 0.8148 (m100) REVERT: E 122 VAL cc_start: 0.8733 (t) cc_final: 0.8482 (m) REVERT: E 140 LYS cc_start: 0.8651 (tptm) cc_final: 0.8450 (tptt) REVERT: E 144 ASP cc_start: 0.8550 (m-30) cc_final: 0.8212 (m-30) REVERT: L 1 MET cc_start: 0.8995 (mtp) cc_final: 0.8742 (mtp) REVERT: L 35 LYS cc_start: 0.8385 (pttp) cc_final: 0.7954 (pttp) REVERT: L 76 LYS cc_start: 0.8386 (pttt) cc_final: 0.8066 (pttm) outliers start: 74 outliers final: 62 residues processed: 554 average time/residue: 0.1875 time to fit residues: 156.3329 Evaluate side-chains 565 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 498 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1046 LYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 118 optimal weight: 0.8980 chunk 165 optimal weight: 0.0270 chunk 289 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 268 optimal weight: 0.0770 chunk 146 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** L 79 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 = 0.3351 r_free = 0.3351 target = 0.079631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064199 restraints weight = 69202.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066115 restraints weight = 35113.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067376 restraints weight = 22906.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068174 restraints weight = 17371.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068669 restraints weight = 14594.598| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24358 Z= 0.135 Angle : 0.663 9.680 32904 Z= 0.334 Chirality : 0.042 0.233 3644 Planarity : 0.005 0.101 4213 Dihedral : 6.868 154.726 3239 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.62 % Allowed : 21.75 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2920 helix: 1.63 (0.15), residues: 1340 sheet: 0.32 (0.28), residues: 334 loop : -1.21 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1292 TYR 0.051 0.001 TYR D 152 PHE 0.023 0.001 PHE D 395 TRP 0.042 0.001 TRP L 75 HIS 0.009 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (24349) covalent geometry : angle 0.65773 / 0.33 (32892) hydrogen bonds : bond 0.04843 / 3.25 ( 1050) hydrogen bonds : angle 3.96701 / 2.74 ( 3036) metal coordination : bond 0.00513 / 0.31 ( 8) metal coordination : angle 4.56891 / 2.47 ( 12) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8701 (ttm) cc_final: 0.8397 (ttm) REVERT: A 307 GLN cc_start: 0.7111 (mp10) cc_final: 0.6895 (mp10) REVERT: A 344 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6560 (mm-30) REVERT: A 347 GLN cc_start: 0.8316 (tp40) cc_final: 0.8104 (tp40) REVERT: A 372 THR cc_start: 0.8362 (p) cc_final: 0.8114 (t) REVERT: A 385 ARG cc_start: 0.5314 (ttp-170) cc_final: 0.5061 (ptp-170) REVERT: A 472 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5760 (pm20) REVERT: A 486 ASN cc_start: 0.7740 (t0) cc_final: 0.7177 (t0) REVERT: A 516 MET cc_start: 0.8239 (tmm) cc_final: 0.7396 (tmm) REVERT: A 561 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7562 (mtm-85) REVERT: A 620 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 622 PHE cc_start: 0.8019 (m-80) cc_final: 0.7639 (m-80) REVERT: A 636 LYS cc_start: 0.8195 (mttt) cc_final: 0.7956 (mtpt) REVERT: A 639 ASP cc_start: 0.7602 (p0) cc_final: 0.7363 (p0) REVERT: A 649 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: A 687 SER cc_start: 0.8687 (p) cc_final: 0.8378 (t) REVERT: A 688 VAL cc_start: 0.8720 (t) cc_final: 0.8163 (p) REVERT: A 796 GLN cc_start: 0.7483 (mp10) cc_final: 0.6910 (mp10) REVERT: A 830 ASP cc_start: 0.7764 (m-30) cc_final: 0.7406 (m-30) REVERT: A 836 ASP cc_start: 0.7725 (p0) cc_final: 0.7396 (p0) REVERT: A 849 ASP cc_start: 0.7810 (p0) cc_final: 0.7510 (p0) REVERT: B 275 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 558 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: B 941 LYS cc_start: 0.4143 (tttt) cc_final: 0.2370 (pttp) REVERT: B 952 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7229 (mmt-90) REVERT: B 969 GLU cc_start: 0.7965 (mp0) cc_final: 0.7744 (mp0) REVERT: B 1020 TRP cc_start: 0.8689 (m100) cc_final: 0.7764 (m100) REVERT: B 1022 SER cc_start: 0.8492 (m) cc_final: 0.8152 (p) REVERT: B 1078 LYS cc_start: 0.7563 (tptp) cc_final: 0.7331 (tptt) REVERT: B 1276 SER cc_start: 0.8339 (m) cc_final: 0.7562 (p) REVERT: B 1290 TYR cc_start: 0.7076 (m-80) cc_final: 0.6423 (m-80) REVERT: B 1300 VAL cc_start: 0.8530 (t) cc_final: 0.8170 (m) REVERT: B 1334 ASP cc_start: 0.7270 (t0) cc_final: 0.7012 (t0) REVERT: C 129 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7124 (tm-30) REVERT: C 181 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 206 LYS cc_start: 0.9276 (mtmt) cc_final: 0.9053 (mttt) REVERT: C 242 GLU cc_start: 0.7486 (mp0) cc_final: 0.7202 (mp0) REVERT: C 245 ASP cc_start: 0.7441 (t70) cc_final: 0.6933 (t70) REVERT: C 247 LEU cc_start: 0.8376 (tp) cc_final: 0.8110 (tp) REVERT: C 263 LYS cc_start: 0.7501 (pptt) cc_final: 0.6948 (ttpp) REVERT: C 285 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 351 LEU cc_start: 0.7089 (mp) cc_final: 0.6813 (pp) REVERT: C 369 MET cc_start: 0.8283 (mtm) cc_final: 0.7923 (ppp) REVERT: C 433 LEU cc_start: 0.8962 (mt) cc_final: 0.8701 (tp) REVERT: C 436 LEU cc_start: 0.8359 (mt) cc_final: 0.8057 (mt) REVERT: D 118 MET cc_start: 0.7477 (mmm) cc_final: 0.7138 (mtm) REVERT: D 145 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8279 (pttm) REVERT: D 169 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7865 (p0) REVERT: D 322 ASP cc_start: 0.7858 (t0) cc_final: 0.7591 (t0) REVERT: D 330 CYS cc_start: 0.8124 (t) cc_final: 0.7478 (p) REVERT: D 359 CYS cc_start: 0.7844 (m) cc_final: 0.7586 (p) REVERT: D 378 LEU cc_start: 0.8956 (tp) cc_final: 0.8595 (tt) REVERT: E 38 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 40 TYR cc_start: 0.8223 (t80) cc_final: 0.7869 (t80) REVERT: E 48 PHE cc_start: 0.8474 (p90) cc_final: 0.8155 (p90) REVERT: E 105 TRP cc_start: 0.8561 (m100) cc_final: 0.8126 (m100) REVERT: E 122 VAL cc_start: 0.8738 (t) cc_final: 0.8503 (m) REVERT: E 144 ASP cc_start: 0.8555 (m-30) cc_final: 0.8240 (m-30) REVERT: L 1 MET cc_start: 0.8996 (mtp) cc_final: 0.8743 (mtp) REVERT: L 35 LYS cc_start: 0.8394 (pttp) cc_final: 0.7971 (pttp) outliers start: 69 outliers final: 59 residues processed: 541 average time/residue: 0.1917 time to fit residues: 154.8930 Evaluate side-chains 561 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 497 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 276 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 62 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 127 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 265 optimal weight: 0.0770 chunk 109 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1152 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064526 restraints weight = 68619.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066451 restraints weight = 34828.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067693 restraints weight = 22694.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068469 restraints weight = 17299.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068980 restraints weight = 14590.562| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24358 Z= 0.131 Angle : 0.655 9.778 32904 Z= 0.330 Chirality : 0.042 0.239 3644 Planarity : 0.004 0.097 4213 Dihedral : 6.807 154.284 3239 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 2.62 % Allowed : 21.94 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: 0.49 (0.16), residues: 2920 helix: 1.65 (0.15), residues: 1341 sheet: 0.39 (0.28), residues: 327 loop : -1.20 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1292 TYR 0.051 0.001 TYR D 152 PHE 0.022 0.001 PHE D 395 TRP 0.030 0.001 TRP L 75 HIS 0.004 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24349) covalent geometry : angle 0.64990 / 0.33 (32892) hydrogen bonds : bond 0.04655 / 3.14 ( 1050) hydrogen bonds : angle 3.94315 / 2.72 ( 3036) metal coordination : bond 0.00511 / 0.30 ( 8) metal coordination : angle 4.47734 / 2.42 ( 12) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.12 seconds wall clock time: 88 minutes 53.43 seconds (5333.43 seconds total)