Starting phenix.real_space_refine on Fri Feb 6 20:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nv9_49831/02_2026/9nv9_49831.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.091 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 147 5.16 5 C 17323 2.51 5 N 4777 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27415 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3855 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 4 Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3863 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 22, 'TRANS': 471} Chain breaks: 3 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3863 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 22, 'TRANS': 471} Chain breaks: 3 Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3855 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 4 Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3855 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 4 Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3855 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 4 Chain: "G" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3863 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 22, 'TRANS': 471} Chain breaks: 3 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.33, per 1000 atoms: 0.23 Number of scatterers: 27415 At special positions: 0 Unit cell: (108.504, 154.536, 155.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 147 16.00 P 35 15.00 O 5133 8.00 N 4777 7.00 C 17323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 943.4 milliseconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6404 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 15 sheets defined 60.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.747A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.703A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.756A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.981A pdb=" N ALA A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.742A pdb=" N ARG A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.361A pdb=" N ILE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.688A pdb=" N ILE A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.523A pdb=" N LEU A 383 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.508A pdb=" N ARG A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 3.851A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 458 removed outlier: 3.922A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 503 removed outlier: 4.385A pdb=" N TYR A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 removed outlier: 3.925A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.885A pdb=" N LEU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.725A pdb=" N LYS A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 577 through 593 removed outlier: 4.254A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 619 through 630 removed outlier: 4.080A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.795A pdb=" N LEU A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.514A pdb=" N LEU A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.697A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 718 removed outlier: 3.679A pdb=" N LEU A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 736 through 736 No H-bonds generated for 'chain 'A' and resid 736 through 736' Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.971A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.642A pdb=" N VAL B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.793A pdb=" N ALA B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.603A pdb=" N ARG B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.680A pdb=" N ILE B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.524A pdb=" N LEU B 383 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.845A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 458 removed outlier: 3.869A pdb=" N LEU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.589A pdb=" N PHE B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 4.630A pdb=" N TYR B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.941A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.939A pdb=" N LEU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.959A pdb=" N LYS B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 4.141A pdb=" N GLN B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.506A pdb=" N LEU B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 609 " --> pdb=" O ILE B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.934A pdb=" N LEU B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.914A pdb=" N LEU B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 684 Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.754A pdb=" N GLN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.633A pdb=" N GLU B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 736 No H-bonds generated for 'chain 'B' and resid 736 through 736' Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.865A pdb=" N MET C 218 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 236 removed outlier: 3.619A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.579A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 removed outlier: 3.528A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.798A pdb=" N LYS C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.714A pdb=" N ALA C 300 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.601A pdb=" N ARG C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 329 through 334 removed outlier: 4.372A pdb=" N ILE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 334' Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.687A pdb=" N ILE C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.520A pdb=" N LEU C 383 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 411 Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.503A pdb=" N ARG C 415 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.849A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 458 removed outlier: 3.955A pdb=" N LEU C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.558A pdb=" N PHE C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 503 removed outlier: 4.446A pdb=" N TYR C 499 " --> pdb=" O ASN C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.886A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 4.085A pdb=" N LEU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.863A pdb=" N GLN C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 removed outlier: 3.630A pdb=" N LEU C 608 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 609 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 604 through 610' Processing helix chain 'C' and resid 619 through 630 removed outlier: 3.720A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 629 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 653 removed outlier: 3.919A pdb=" N LEU C 652 " --> pdb=" O ARG C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 684 removed outlier: 3.505A pdb=" N LEU C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 699 removed outlier: 3.838A pdb=" N GLN C 697 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 718 removed outlier: 3.622A pdb=" N MET C 716 " --> pdb=" O MET C 712 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 718 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 735 removed outlier: 3.659A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 736 No H-bonds generated for 'chain 'C' and resid 736 through 736' Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'D' and resid 223 through 236 removed outlier: 3.766A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.514A pdb=" N VAL D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.512A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.543A pdb=" N ASN D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 removed outlier: 4.134A pdb=" N ALA D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.829A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 351 through 359 Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.683A pdb=" N ILE D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 removed outlier: 3.534A pdb=" N LEU D 383 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 411 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.860A pdb=" N LEU D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 458 removed outlier: 4.065A pdb=" N LEU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.973A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.038A pdb=" N LEU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.964A pdb=" N LYS D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 573 " --> pdb=" O PRO D 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 577 through 592 removed outlier: 4.074A pdb=" N GLN D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 592 " --> pdb=" O ILE D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 604 through 609 removed outlier: 3.674A pdb=" N LEU D 608 " --> pdb=" O ASP D 604 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 609 " --> pdb=" O ILE D 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 604 through 609' Processing helix chain 'D' and resid 620 through 630 removed outlier: 3.536A pdb=" N LEU D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 removed outlier: 3.576A pdb=" N LEU D 652 " --> pdb=" O ARG D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.733A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 717 Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.676A pdb=" N GLU D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 736 No H-bonds generated for 'chain 'D' and resid 736 through 736' Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.849A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 239 " --> pdb=" O PHE E 235 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 249 removed outlier: 3.660A pdb=" N VAL E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 removed outlier: 3.646A pdb=" N GLN E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 292 Processing helix chain 'E' and resid 296 through 316 removed outlier: 4.264A pdb=" N ALA E 300 " --> pdb=" O GLY E 296 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.678A pdb=" N ILE E 379 " --> pdb=" O PRO E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.531A pdb=" N LEU E 383 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 Processing helix chain 'E' and resid 411 through 418 removed outlier: 3.509A pdb=" N ARG E 415 " --> pdb=" O THR E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 removed outlier: 3.842A pdb=" N LEU E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 458 removed outlier: 4.049A pdb=" N LEU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 503 removed outlier: 4.385A pdb=" N TYR E 499 " --> pdb=" O ASN E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 531 removed outlier: 3.830A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.170A pdb=" N LEU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.989A pdb=" N GLN E 583 " --> pdb=" O THR E 579 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 591 " --> pdb=" O LYS E 587 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 592 " --> pdb=" O ILE E 588 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 removed outlier: 3.692A pdb=" N LEU E 608 " --> pdb=" O ASP E 604 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 609 " --> pdb=" O ILE E 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 604 through 609' Processing helix chain 'E' and resid 619 through 630 removed outlier: 3.653A pdb=" N LEU E 623 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 655 removed outlier: 3.941A pdb=" N LEU E 652 " --> pdb=" O ARG E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 684 Processing helix chain 'E' and resid 690 through 699 removed outlier: 3.883A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 718 removed outlier: 4.065A pdb=" N LEU E 718 " --> pdb=" O ILE E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 720 No H-bonds generated for 'chain 'E' and resid 719 through 720' Processing helix chain 'E' and resid 721 through 723 No H-bonds generated for 'chain 'E' and resid 721 through 723' Processing helix chain 'E' and resid 724 through 735 Processing helix chain 'E' and resid 736 through 736 No H-bonds generated for 'chain 'E' and resid 736 through 736' Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 223 through 236 removed outlier: 3.827A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.557A pdb=" N VAL F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 277 removed outlier: 3.650A pdb=" N LEU F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 296 through 306 removed outlier: 3.773A pdb=" N ALA F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 302 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.573A pdb=" N GLN F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 359 Processing helix chain 'F' and resid 380 through 384 removed outlier: 3.531A pdb=" N LEU F 383 " --> pdb=" O ASP F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 Processing helix chain 'F' and resid 411 through 418 Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.842A pdb=" N LEU F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 458 removed outlier: 3.934A pdb=" N LEU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.522A pdb=" N PHE F 480 " --> pdb=" O THR F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 503 Processing helix chain 'F' and resid 511 through 531 removed outlier: 3.920A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.958A pdb=" N LEU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 559 " --> pdb=" O LYS F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 573 removed outlier: 3.734A pdb=" N LYS F 572 " --> pdb=" O SER F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 593 removed outlier: 4.337A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 592 " --> pdb=" O ILE F 588 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR F 593 " --> pdb=" O PHE F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 removed outlier: 3.538A pdb=" N LEU F 608 " --> pdb=" O ASP F 604 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 609 " --> pdb=" O ILE F 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 604 through 609' Processing helix chain 'F' and resid 619 through 630 removed outlier: 3.756A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 655 removed outlier: 3.843A pdb=" N LEU F 652 " --> pdb=" O ARG F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 699 removed outlier: 3.931A pdb=" N GLN F 697 " --> pdb=" O THR F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 718 removed outlier: 4.010A pdb=" N LEU F 718 " --> pdb=" O ILE F 714 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 735 Processing helix chain 'F' and resid 736 through 736 No H-bonds generated for 'chain 'F' and resid 736 through 736' Processing helix chain 'G' and resid 215 through 219 Processing helix chain 'G' and resid 223 through 235 Processing helix chain 'G' and resid 236 through 239 removed outlier: 3.759A pdb=" N VAL G 239 " --> pdb=" O ALA G 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 236 through 239' Processing helix chain 'G' and resid 241 through 249 Processing helix chain 'G' and resid 265 through 278 removed outlier: 3.545A pdb=" N LEU G 269 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS G 275 " --> pdb=" O ARG G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.722A pdb=" N ALA G 300 " --> pdb=" O GLY G 296 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE G 302 " --> pdb=" O SER G 298 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE G 306 " --> pdb=" O ILE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 314 removed outlier: 4.225A pdb=" N ARG G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 333 Processing helix chain 'G' and resid 351 through 359 Processing helix chain 'G' and resid 375 through 379 removed outlier: 3.527A pdb=" N LEU G 378 " --> pdb=" O ARG G 375 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 379 " --> pdb=" O PRO G 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 375 through 379' Processing helix chain 'G' and resid 380 through 384 removed outlier: 3.524A pdb=" N LEU G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 411 Processing helix chain 'G' and resid 411 through 418 Processing helix chain 'G' and resid 425 through 433 removed outlier: 3.836A pdb=" N LEU G 429 " --> pdb=" O ASP G 425 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 431 " --> pdb=" O LYS G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 458 removed outlier: 3.823A pdb=" N LEU G 441 " --> pdb=" O SER G 437 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 442 " --> pdb=" O GLY G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 503 removed outlier: 4.224A pdb=" N TYR G 499 " --> pdb=" O ASN G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 531 removed outlier: 3.908A pdb=" N THR G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 559 removed outlier: 3.902A pdb=" N LEU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 573 removed outlier: 3.502A pdb=" N LYS G 572 " --> pdb=" O SER G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 592 removed outlier: 3.754A pdb=" N GLN G 583 " --> pdb=" O THR G 579 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP G 591 " --> pdb=" O LYS G 587 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA G 592 " --> pdb=" O ILE G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 595 No H-bonds generated for 'chain 'G' and resid 593 through 595' Processing helix chain 'G' and resid 604 through 610 removed outlier: 3.719A pdb=" N LEU G 608 " --> pdb=" O ASP G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 630 removed outlier: 3.750A pdb=" N LEU G 623 " --> pdb=" O SER G 619 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 629 " --> pdb=" O ALA G 625 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU G 630 " --> pdb=" O LEU G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 655 removed outlier: 4.112A pdb=" N LEU G 652 " --> pdb=" O ARG G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 684 Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.744A pdb=" N GLN G 697 " --> pdb=" O THR G 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 718 removed outlier: 3.881A pdb=" N MET G 716 " --> pdb=" O MET G 712 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU G 718 " --> pdb=" O ILE G 714 " (cutoff:3.500A) Processing helix chain 'G' and resid 724 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 286 removed outlier: 3.521A pdb=" N ASP A 328 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 370 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 568 removed outlier: 3.504A pdb=" N THR A 645 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 541 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 665 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 540 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 280 through 284 removed outlier: 6.594A pdb=" N GLU B 281 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE B 326 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 283 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 565 through 568 removed outlier: 6.550A pdb=" N VAL B 600 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR B 645 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 602 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 539 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 646 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 541 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER B 538 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE B 665 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 540 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.689A pdb=" N LYS C 283 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 566 through 568 removed outlier: 3.517A pdb=" N THR C 645 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 541 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE C 665 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 540 " --> pdb=" O ILE C 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 283 through 284 removed outlier: 6.563A pdb=" N LYS D 283 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 372 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 256 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR D 373 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU D 258 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 566 through 568 removed outlier: 8.458A pdb=" N ILE D 665 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 540 " --> pdb=" O ILE D 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 283 through 285 removed outlier: 6.664A pdb=" N LYS E 283 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 370 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET E 372 " --> pdb=" O PHE E 327 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE E 256 " --> pdb=" O GLY E 371 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR E 373 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 258 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 565 through 568 removed outlier: 3.500A pdb=" N THR E 645 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 537 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY E 644 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 539 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR E 646 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 541 " --> pdb=" O THR E 646 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR E 663 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 538 " --> pdb=" O THR E 663 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ILE E 665 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU E 540 " --> pdb=" O ILE E 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 283 through 286 removed outlier: 6.696A pdb=" N LYS F 283 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP F 328 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 285 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE F 256 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR F 373 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU F 258 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 566 through 568 removed outlier: 7.299A pdb=" N VAL F 539 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR F 646 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 541 " --> pdb=" O THR F 646 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE F 665 " --> pdb=" O SER F 538 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 540 " --> pdb=" O ILE F 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 612 through 612 removed outlier: 3.624A pdb=" N ARG F 617 " --> pdb=" O VAL F 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 283 through 284 removed outlier: 6.235A pdb=" N LYS G 283 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU G 368 " --> pdb=" O HIS G 323 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 370 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N MET G 393 " --> pdb=" O GLY G 255 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU G 257 " --> pdb=" O MET G 393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 566 through 568 removed outlier: 6.573A pdb=" N VAL G 600 " --> pdb=" O ILE G 643 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE G 665 " --> pdb=" O SER G 538 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU G 540 " --> pdb=" O ILE G 665 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3378 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: 4.76 Time building geometry restraints manager: 2.63 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: 8777 1.34 - 1.46: 3490 1.46 - 1.58: 15256 1.58 - 1.70: 49 1.70 - 1.82: 252 Bond restraints: 27824 Sorted by residual: bond pdb=" CB GLN A 336 " pdb=" CG GLN A 336 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CB GLU E 362 " pdb=" CG GLU E 362 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB GLN E 336 " pdb=" CG GLN E 336 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB GLN F 336 " pdb=" CG GLN F 336 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" CB GLU A 226 " pdb=" CG GLU A 226 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+00 ... (remaining 27819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 36280 1.93 - 3.86: 976 3.86 - 5.80: 233 5.80 - 7.73: 34 7.73 - 9.66: 4 Bond angle restraints: 37527 Sorted by residual: angle pdb=" O3A ATP C 802 " pdb=" PA ATP C 802 " pdb=" O5' ATP C 802 " ideal model delta sigma weight residual 102.67 112.33 -9.66 2.38e+00 1.77e-01 1.65e+01 angle pdb=" C4' ATP E 802 " pdb=" C5' ATP E 802 " pdb=" O5' ATP E 802 " ideal model delta sigma weight residual 108.83 117.65 -8.82 2.33e+00 1.85e-01 1.43e+01 angle pdb=" O3A ATP B 802 " pdb=" PA ATP B 802 " pdb=" O5' ATP B 802 " ideal model delta sigma weight residual 102.67 110.91 -8.24 2.38e+00 1.77e-01 1.20e+01 angle pdb=" CB GLU A 226 " pdb=" CG GLU A 226 " pdb=" CD GLU A 226 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 angle pdb=" C4' ATP D 802 " pdb=" C5' ATP D 802 " pdb=" O5' ATP D 802 " ideal model delta sigma weight residual 108.83 116.34 -7.51 2.33e+00 1.85e-01 1.04e+01 ... (remaining 37522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 16704 27.83 - 55.65: 562 55.65 - 83.48: 69 83.48 - 111.31: 6 111.31 - 139.13: 2 Dihedral angle restraints: 17343 sinusoidal: 7468 harmonic: 9875 Sorted by residual: dihedral pdb=" C2' ADP E 801 " pdb=" C1' ADP E 801 " pdb=" N9 ADP E 801 " pdb=" C4 ADP E 801 " ideal model delta sinusoidal sigma weight residual 91.55 -129.32 -139.13 1 2.00e+01 2.50e-03 4.21e+01 dihedral pdb=" C2' ADP D 801 " pdb=" C1' ADP D 801 " pdb=" N9 ADP D 801 " pdb=" C4 ADP D 801 " ideal model delta sinusoidal sigma weight residual 91.55 -154.34 -114.12 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" C4' ADP C 801 " pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual 180.00 -104.32 -75.68 1 2.00e+01 2.50e-03 1.81e+01 ... (remaining 17340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2692 0.037 - 0.074: 1135 0.074 - 0.111: 326 0.111 - 0.148: 140 0.148 - 0.186: 22 Chirality restraints: 4315 Sorted by residual: chirality pdb=" CA VAL E 285 " pdb=" N VAL E 285 " pdb=" C VAL E 285 " pdb=" CB VAL E 285 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE C 256 " pdb=" N ILE C 256 " pdb=" C ILE C 256 " pdb=" CB ILE C 256 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 4312 not shown) Planarity restraints: 4755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 729 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PHE A 729 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE A 729 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 730 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 727 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ARG E 727 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG E 727 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS E 728 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 268 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU D 268 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU D 268 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU D 269 " 0.019 2.00e-02 2.50e+03 ... (remaining 4752 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 10687 2.92 - 3.41: 26671 3.41 - 3.91: 37883 3.91 - 4.40: 41732 4.40 - 4.90: 73350 Nonbonded interactions: 190323 Sorted by model distance: nonbonded pdb=" OG1 THR D 672 " pdb=" OE1 GLN D 675 " model vdw 2.421 3.040 nonbonded pdb=" O GLY F 644 " pdb=" OG1 THR F 645 " model vdw 2.443 3.040 nonbonded pdb=" O GLY A 644 " pdb=" OG1 THR A 645 " model vdw 2.459 3.040 nonbonded pdb=" O ASP G 590 " pdb=" OD1 ASP G 590 " model vdw 2.465 3.040 nonbonded pdb=" OG1 THR B 672 " pdb=" OE1 GLN B 675 " model vdw 2.472 3.040 ... (remaining 190318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 215 through 327 or resid 329 through 609 or resid 611 thro \ ugh 687 or resid 689 through 802)) selection = (chain 'B' and (resid 215 through 327 or resid 329 through 398 or resid 400 thro \ ugh 609 or resid 611 through 687 or resid 689 through 802)) selection = (chain 'C' and (resid 215 through 327 or resid 329 through 398 or resid 400 thro \ ugh 609 or resid 611 through 687 or resid 689 through 802)) selection = (chain 'D' and (resid 215 through 398 or resid 400 through 609 or resid 611 thro \ ugh 687 or resid 689 through 802)) selection = (chain 'E' and (resid 215 through 327 or resid 329 through 398 or resid 400 thro \ ugh 609 or resid 611 through 802)) selection = (chain 'F' and (resid 215 through 327 or resid 329 through 398 or resid 400 thro \ ugh 687 or resid 689 through 802)) selection = (chain 'G' and (resid 215 through 327 or resid 329 through 398 or resid 400 thro \ ugh 609 or resid 611 through 687 or resid 689 through 802)) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.830 Find NCS groups from input model: 0.830 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.048 27824 Z= 0.189 Angle : 0.820 9.661 37527 Z= 0.421 Chirality : 0.048 0.186 4315 Planarity : 0.005 0.041 4755 Dihedral : 13.680 139.134 10939 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.25 % Allowed : 8.25 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3390 helix: 0.70 (0.13), residues: 1661 sheet: -1.31 (0.23), residues: 437 loop : -0.60 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 691 TYR 0.014 0.001 TYR F 499 PHE 0.023 0.001 PHE D 436 TRP 0.006 0.001 TRP C 704 HIS 0.013 0.001 HIS C 546 Details of bonding type rmsd covalent geometry : bond 0.00421 (27824) covalent geometry : angle 0.81952 (37527) hydrogen bonds : bond 0.18603 ( 1166) hydrogen bonds : angle 5.90802 ( 3378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 304 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.7236 (mpp) cc_final: 0.6730 (mtp) REVERT: A 235 PHE cc_start: 0.8067 (m-80) cc_final: 0.7814 (m-10) REVERT: A 655 MET cc_start: 0.8189 (mtm) cc_final: 0.7988 (mtm) REVERT: A 712 MET cc_start: 0.7834 (tpp) cc_final: 0.7510 (tpp) REVERT: B 218 MET cc_start: 0.7321 (mpp) cc_final: 0.7103 (mpp) REVERT: B 235 PHE cc_start: 0.8623 (m-80) cc_final: 0.8345 (m-10) REVERT: B 364 LEU cc_start: 0.7460 (mp) cc_final: 0.7054 (mp) REVERT: C 393 MET cc_start: 0.8112 (mmt) cc_final: 0.7854 (mmt) REVERT: D 218 MET cc_start: 0.8451 (mtp) cc_final: 0.7992 (mtt) REVERT: D 393 MET cc_start: 0.8162 (mmt) cc_final: 0.7942 (mmp) REVERT: D 542 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7971 (pp20) REVERT: D 724 TYR cc_start: 0.8472 (m-80) cc_final: 0.8146 (m-10) REVERT: E 327 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: F 504 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6840 (mtt) REVERT: F 657 MET cc_start: 0.9058 (ttm) cc_final: 0.8819 (ttt) REVERT: G 224 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: G 499 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.5849 (m-10) outliers start: 96 outliers final: 44 residues processed: 389 average time/residue: 0.1841 time to fit residues: 110.3567 Evaluate side-chains 212 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 711 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 504 MET Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 377 ASP Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 499 TYR Chi-restraints excluded: chain G residue 598 SER Chi-restraints excluded: chain G residue 711 LEU Chi-restraints excluded: chain G residue 723 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 546 HIS C 454 ASN C 546 HIS C 636 GLN F 454 ASN G 418 GLN G 454 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079921 restraints weight = 54089.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081560 restraints weight = 32858.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082122 restraints weight = 25195.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082281 restraints weight = 23713.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082558 restraints weight = 21703.423| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27824 Z= 0.170 Angle : 0.638 8.043 37527 Z= 0.322 Chirality : 0.046 0.177 4315 Planarity : 0.004 0.049 4755 Dihedral : 11.173 137.097 4068 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.84 % Allowed : 10.86 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3390 helix: 1.20 (0.13), residues: 1672 sheet: -0.84 (0.24), residues: 429 loop : -0.27 (0.19), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 303 TYR 0.016 0.001 TYR A 499 PHE 0.014 0.001 PHE A 235 TRP 0.011 0.001 TRP F 704 HIS 0.005 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00410 (27824) covalent geometry : angle 0.63847 (37527) hydrogen bonds : bond 0.05513 ( 1166) hydrogen bonds : angle 4.20058 ( 3378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 393 MET cc_start: 0.7574 (mmm) cc_final: 0.7312 (mmm) REVERT: A 712 MET cc_start: 0.7858 (tpp) cc_final: 0.7466 (tpp) REVERT: B 218 MET cc_start: 0.8062 (mpp) cc_final: 0.7820 (mpp) REVERT: B 235 PHE cc_start: 0.8488 (m-80) cc_final: 0.8267 (m-10) REVERT: B 353 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: B 675 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: D 218 MET cc_start: 0.8604 (mtp) cc_final: 0.8128 (mtt) REVERT: D 542 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7981 (pp20) REVERT: E 218 MET cc_start: 0.8716 (mtm) cc_final: 0.8457 (ttm) REVERT: E 327 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: E 440 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: E 558 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: E 657 MET cc_start: 0.9312 (ttm) cc_final: 0.8741 (ttt) REVERT: G 720 MET cc_start: 0.8645 (mmm) cc_final: 0.8354 (mtp) outliers start: 84 outliers final: 47 residues processed: 247 average time/residue: 0.1612 time to fit residues: 65.4221 Evaluate side-chains 207 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 598 SER Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain G residue 711 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 54 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS E 272 GLN E 530 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077986 restraints weight = 55023.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079518 restraints weight = 32951.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080476 restraints weight = 25242.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.080866 restraints weight = 22196.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081310 restraints weight = 20302.318| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 27824 Z= 0.215 Angle : 0.647 8.022 37527 Z= 0.324 Chirality : 0.047 0.169 4315 Planarity : 0.005 0.045 4755 Dihedral : 11.019 135.562 4014 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.26 % Allowed : 11.33 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3390 helix: 1.21 (0.13), residues: 1670 sheet: -0.88 (0.23), residues: 437 loop : -0.39 (0.19), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 314 TYR 0.015 0.002 TYR D 724 PHE 0.017 0.001 PHE F 564 TRP 0.010 0.002 TRP F 704 HIS 0.005 0.001 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00542 (27824) covalent geometry : angle 0.64672 (37527) hydrogen bonds : bond 0.05685 ( 1166) hydrogen bonds : angle 4.07621 ( 3378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 156 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8274 (tpp) cc_final: 0.7914 (tpp) REVERT: A 393 MET cc_start: 0.7806 (mmm) cc_final: 0.7543 (mmm) REVERT: B 218 MET cc_start: 0.8015 (mpp) cc_final: 0.7363 (mtm) REVERT: B 235 PHE cc_start: 0.8583 (m-80) cc_final: 0.8329 (m-10) REVERT: B 353 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: B 675 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: D 218 MET cc_start: 0.8658 (mtp) cc_final: 0.8401 (mtp) REVERT: D 542 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8079 (pp20) REVERT: D 675 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: E 218 MET cc_start: 0.8851 (mtm) cc_final: 0.8423 (mtm) REVERT: E 327 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: E 393 MET cc_start: 0.7548 (mmm) cc_final: 0.7124 (mmt) REVERT: E 440 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: E 657 MET cc_start: 0.9253 (ttm) cc_final: 0.8666 (ttt) REVERT: G 304 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8195 (ptpt) REVERT: G 499 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: G 720 MET cc_start: 0.8656 (mmm) cc_final: 0.8213 (mtp) outliers start: 126 outliers final: 82 residues processed: 268 average time/residue: 0.1456 time to fit residues: 66.1621 Evaluate side-chains 239 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 150 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 558 GLU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 311 GLU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 499 TYR Chi-restraints excluded: chain G residue 598 SER Chi-restraints excluded: chain G residue 663 THR Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain G residue 711 LEU Chi-restraints excluded: chain G residue 723 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080820 restraints weight = 53805.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081962 restraints weight = 33539.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082446 restraints weight = 26863.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082993 restraints weight = 25110.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083245 restraints weight = 22351.929| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27824 Z= 0.125 Angle : 0.553 6.952 37527 Z= 0.274 Chirality : 0.043 0.157 4315 Planarity : 0.004 0.045 4755 Dihedral : 10.626 133.251 4012 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.15 % Allowed : 13.36 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3390 helix: 1.46 (0.13), residues: 1679 sheet: -0.63 (0.24), residues: 441 loop : -0.26 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 303 TYR 0.008 0.001 TYR A 502 PHE 0.009 0.001 PHE A 306 TRP 0.009 0.001 TRP F 704 HIS 0.003 0.001 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00301 (27824) covalent geometry : angle 0.55345 (37527) hydrogen bonds : bond 0.04046 ( 1166) hydrogen bonds : angle 3.65689 ( 3378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 160 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8221 (tpp) cc_final: 0.7783 (tpp) REVERT: A 393 MET cc_start: 0.7672 (mmm) cc_final: 0.7457 (mmm) REVERT: B 218 MET cc_start: 0.7808 (mpp) cc_final: 0.7271 (mtm) REVERT: B 240 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6183 (t80) REVERT: B 675 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7221 (mt0) REVERT: D 218 MET cc_start: 0.8635 (mtp) cc_final: 0.8377 (mtp) REVERT: D 440 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: D 675 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: E 327 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: E 440 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: E 657 MET cc_start: 0.9186 (ttm) cc_final: 0.8530 (ttt) REVERT: G 304 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8211 (ptpt) REVERT: G 720 MET cc_start: 0.8412 (mmm) cc_final: 0.8129 (mtp) outliers start: 93 outliers final: 59 residues processed: 239 average time/residue: 0.1491 time to fit residues: 60.0496 Evaluate side-chains 216 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 606 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 311 GLU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 598 SER Chi-restraints excluded: chain G residue 672 THR Chi-restraints excluded: chain G residue 711 LEU Chi-restraints excluded: chain G residue 723 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 48 optimal weight: 4.9990 chunk 162 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 203 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081239 restraints weight = 53606.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082716 restraints weight = 31537.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083524 restraints weight = 23297.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084341 restraints weight = 21214.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084370 restraints weight = 18876.873| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 27824 Z= 0.110 Angle : 0.527 7.565 37527 Z= 0.258 Chirality : 0.043 0.276 4315 Planarity : 0.004 0.044 4755 Dihedral : 10.097 129.862 4000 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.25 % Allowed : 14.47 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3390 helix: 1.60 (0.13), residues: 1682 sheet: -0.43 (0.24), residues: 441 loop : -0.20 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 303 TYR 0.009 0.001 TYR E 502 PHE 0.013 0.001 PHE A 235 TRP 0.008 0.001 TRP C 704 HIS 0.004 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00261 (27824) covalent geometry : angle 0.52699 (37527) hydrogen bonds : bond 0.03660 ( 1166) hydrogen bonds : angle 3.50158 ( 3378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 163 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8286 (tpp) cc_final: 0.7890 (tpp) REVERT: A 303 ARG cc_start: 0.7802 (tpm170) cc_final: 0.7418 (mtm110) REVERT: A 655 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7775 (mtm) REVERT: B 218 MET cc_start: 0.7889 (mpp) cc_final: 0.7279 (mtm) REVERT: B 240 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6271 (t80) REVERT: B 672 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 675 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: D 218 MET cc_start: 0.8672 (mtp) cc_final: 0.8386 (mtp) REVERT: D 440 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: D 675 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: E 327 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: E 440 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: E 640 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8770 (tp) REVERT: E 657 MET cc_start: 0.9250 (ttm) cc_final: 0.8607 (ttt) REVERT: F 240 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7102 (t80) REVERT: F 305 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8636 (mm) REVERT: G 304 LYS cc_start: 0.8670 (ptpt) cc_final: 0.8250 (ptpt) outliers start: 96 outliers final: 64 residues processed: 244 average time/residue: 0.1592 time to fit residues: 64.8871 Evaluate side-chains 227 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 311 GLU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 598 SER Chi-restraints excluded: chain G residue 723 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 338 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 26 optimal weight: 0.0870 chunk 275 optimal weight: 0.1980 chunk 328 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 173 optimal weight: 0.0770 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 HIS D 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084622 restraints weight = 53617.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.085956 restraints weight = 32446.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086407 restraints weight = 24995.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087079 restraints weight = 24311.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087110 restraints weight = 21028.972| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27824 Z= 0.083 Angle : 0.502 7.870 37527 Z= 0.244 Chirality : 0.041 0.292 4315 Planarity : 0.004 0.063 4755 Dihedral : 9.532 125.657 3997 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.27 % Allowed : 15.76 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3390 helix: 1.75 (0.13), residues: 1689 sheet: -0.18 (0.24), residues: 446 loop : 0.00 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 303 TYR 0.008 0.001 TYR E 502 PHE 0.015 0.001 PHE E 235 TRP 0.007 0.001 TRP C 704 HIS 0.002 0.000 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00173 (27824) covalent geometry : angle 0.50167 (37527) hydrogen bonds : bond 0.02524 ( 1166) hydrogen bonds : angle 3.24880 ( 3378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8219 (tpp) cc_final: 0.7772 (tpp) REVERT: B 218 MET cc_start: 0.7841 (mpp) cc_final: 0.7184 (mtm) REVERT: B 240 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5452 (t80) REVERT: B 657 MET cc_start: 0.8718 (ttm) cc_final: 0.8063 (ttt) REVERT: D 218 MET cc_start: 0.8625 (mtp) cc_final: 0.8311 (mtt) REVERT: D 325 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7329 (mp) REVERT: D 440 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 542 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: E 440 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: E 640 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8618 (tp) REVERT: E 657 MET cc_start: 0.9252 (ttm) cc_final: 0.8652 (ttt) REVERT: F 305 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8693 (mm) REVERT: F 408 HIS cc_start: 0.8336 (t-90) cc_final: 0.8005 (t-170) REVERT: G 304 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8299 (ptpt) outliers start: 67 outliers final: 34 residues processed: 226 average time/residue: 0.1551 time to fit residues: 57.6599 Evaluate side-chains 195 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 457 ILE Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 329 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 287 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 HIS D 278 ASN D 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.083588 restraints weight = 53333.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085141 restraints weight = 32974.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086112 restraints weight = 25044.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086594 restraints weight = 21919.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086686 restraints weight = 20326.250| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27824 Z= 0.089 Angle : 0.502 7.542 37527 Z= 0.243 Chirality : 0.041 0.262 4315 Planarity : 0.004 0.047 4755 Dihedral : 9.045 121.712 3983 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.47 % Allowed : 15.83 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3390 helix: 1.84 (0.13), residues: 1693 sheet: -0.05 (0.24), residues: 445 loop : 0.10 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 303 TYR 0.009 0.001 TYR E 499 PHE 0.014 0.001 PHE B 235 TRP 0.005 0.001 TRP C 704 HIS 0.003 0.000 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00196 (27824) covalent geometry : angle 0.50174 (37527) hydrogen bonds : bond 0.02842 ( 1166) hydrogen bonds : angle 3.20809 ( 3378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8191 (tpp) cc_final: 0.7775 (tpp) REVERT: A 440 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: B 217 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7772 (pttp) REVERT: B 218 MET cc_start: 0.7768 (mpp) cc_final: 0.7445 (mtm) REVERT: B 240 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.4919 (t80) REVERT: D 218 MET cc_start: 0.8613 (mtp) cc_final: 0.8349 (mtp) REVERT: D 325 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7302 (mp) REVERT: D 440 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: D 542 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8089 (pp20) REVERT: E 440 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: E 640 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8621 (tp) REVERT: E 657 MET cc_start: 0.9240 (ttm) cc_final: 0.8644 (ttt) REVERT: F 305 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (mm) REVERT: F 408 HIS cc_start: 0.8338 (t-90) cc_final: 0.8002 (t-170) REVERT: G 304 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8327 (ptpt) outliers start: 73 outliers final: 45 residues processed: 220 average time/residue: 0.1450 time to fit residues: 54.1003 Evaluate side-chains 205 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 327 PHE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 457 ILE Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 672 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 305 optimal weight: 6.9990 chunk 283 optimal weight: 0.0870 chunk 140 optimal weight: 4.9990 chunk 280 optimal weight: 0.0170 chunk 342 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082934 restraints weight = 53860.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083678 restraints weight = 32595.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084473 restraints weight = 26076.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084992 restraints weight = 24789.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085051 restraints weight = 21667.632| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27824 Z= 0.107 Angle : 0.519 10.622 37527 Z= 0.252 Chirality : 0.042 0.244 4315 Planarity : 0.004 0.050 4755 Dihedral : 8.877 118.026 3980 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.27 % Allowed : 16.30 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3390 helix: 1.88 (0.13), residues: 1693 sheet: -0.07 (0.24), residues: 445 loop : 0.05 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 303 TYR 0.012 0.001 TYR E 499 PHE 0.026 0.001 PHE G 240 TRP 0.006 0.001 TRP F 704 HIS 0.002 0.000 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00252 (27824) covalent geometry : angle 0.51910 (37527) hydrogen bonds : bond 0.03319 ( 1166) hydrogen bonds : angle 3.25623 ( 3378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.7315 (mtp) cc_final: 0.6913 (mtp) REVERT: A 276 MET cc_start: 0.8207 (tpp) cc_final: 0.7743 (tpp) REVERT: A 440 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 682 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 217 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7880 (pttp) REVERT: B 218 MET cc_start: 0.7980 (mpp) cc_final: 0.7527 (mtm) REVERT: B 240 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.4923 (t80) REVERT: B 657 MET cc_start: 0.8831 (ttt) cc_final: 0.8298 (ttt) REVERT: D 218 MET cc_start: 0.8644 (mtp) cc_final: 0.8364 (mtp) REVERT: D 325 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7318 (mp) REVERT: D 440 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: D 542 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: D 716 MET cc_start: 0.7290 (tpp) cc_final: 0.7045 (ttt) REVERT: E 440 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: E 640 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8711 (tp) REVERT: E 657 MET cc_start: 0.9257 (ttm) cc_final: 0.8606 (ttt) REVERT: F 408 HIS cc_start: 0.8382 (t-90) cc_final: 0.8031 (t-170) outliers start: 67 outliers final: 52 residues processed: 208 average time/residue: 0.1460 time to fit residues: 51.9111 Evaluate side-chains 208 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 327 PHE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 672 THR Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 280 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 249 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 56 optimal weight: 0.0670 chunk 195 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 311 optimal weight: 3.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 272 GLN F 546 HIS G 456 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080257 restraints weight = 54569.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081487 restraints weight = 37331.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082050 restraints weight = 27736.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082610 restraints weight = 25679.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.082740 restraints weight = 23635.352| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27824 Z= 0.112 Angle : 0.525 9.907 37527 Z= 0.254 Chirality : 0.042 0.225 4315 Planarity : 0.004 0.048 4755 Dihedral : 8.689 111.237 3980 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.43 % Allowed : 16.47 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3390 helix: 1.89 (0.13), residues: 1695 sheet: -0.02 (0.25), residues: 442 loop : 0.01 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 303 TYR 0.017 0.001 TYR E 499 PHE 0.019 0.001 PHE G 240 TRP 0.006 0.001 TRP F 704 HIS 0.003 0.001 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00267 (27824) covalent geometry : angle 0.52497 (37527) hydrogen bonds : bond 0.03439 ( 1166) hydrogen bonds : angle 3.27444 ( 3378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 152 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8268 (tpp) cc_final: 0.7849 (tpp) REVERT: A 440 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: A 682 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 217 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8022 (pttp) REVERT: B 218 MET cc_start: 0.8173 (mpp) cc_final: 0.7642 (mtm) REVERT: B 240 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.4730 (t80) REVERT: B 657 MET cc_start: 0.8960 (ttt) cc_final: 0.8389 (ttt) REVERT: D 218 MET cc_start: 0.8730 (mtp) cc_final: 0.8308 (mtt) REVERT: D 325 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7214 (mp) REVERT: D 440 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: D 542 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8090 (pp20) REVERT: D 720 MET cc_start: 0.8503 (mtp) cc_final: 0.8268 (mtp) REVERT: E 440 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: E 640 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8750 (tp) REVERT: E 657 MET cc_start: 0.9316 (ttm) cc_final: 0.8703 (ttt) REVERT: F 408 HIS cc_start: 0.8409 (t-90) cc_final: 0.8057 (t-170) outliers start: 72 outliers final: 55 residues processed: 213 average time/residue: 0.1490 time to fit residues: 53.7547 Evaluate side-chains 212 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 327 PHE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 672 THR Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 212 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 226 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 255 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081331 restraints weight = 54613.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.082384 restraints weight = 35725.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082994 restraints weight = 28211.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083519 restraints weight = 25043.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.083679 restraints weight = 23050.532| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27824 Z= 0.094 Angle : 0.514 9.882 37527 Z= 0.248 Chirality : 0.041 0.219 4315 Planarity : 0.004 0.050 4755 Dihedral : 8.358 104.720 3980 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.20 % Allowed : 16.88 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3390 helix: 1.91 (0.13), residues: 1695 sheet: 0.03 (0.25), residues: 445 loop : 0.04 (0.19), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 303 TYR 0.016 0.001 TYR E 499 PHE 0.018 0.001 PHE G 240 TRP 0.006 0.001 TRP F 704 HIS 0.002 0.000 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00214 (27824) covalent geometry : angle 0.51415 (37527) hydrogen bonds : bond 0.03031 ( 1166) hydrogen bonds : angle 3.21950 ( 3378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8250 (tpp) cc_final: 0.7787 (tpp) REVERT: A 440 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 682 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 217 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8037 (pttp) REVERT: B 218 MET cc_start: 0.8154 (mpp) cc_final: 0.7677 (mtm) REVERT: B 240 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.4641 (t80) REVERT: B 657 MET cc_start: 0.8948 (ttt) cc_final: 0.8379 (ttt) REVERT: D 218 MET cc_start: 0.8709 (mtp) cc_final: 0.8294 (mtt) REVERT: D 325 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7277 (mp) REVERT: D 440 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: D 542 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8110 (pp20) REVERT: D 720 MET cc_start: 0.8526 (mtp) cc_final: 0.8288 (mtp) REVERT: E 440 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: E 640 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8727 (tp) REVERT: E 657 MET cc_start: 0.9290 (ttm) cc_final: 0.8718 (ttt) REVERT: F 408 HIS cc_start: 0.8384 (t-90) cc_final: 0.8036 (t-170) outliers start: 65 outliers final: 54 residues processed: 208 average time/residue: 0.1436 time to fit residues: 50.8904 Evaluate side-chains 213 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 598 SER Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 598 SER Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 682 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 327 PHE Chi-restraints excluded: chain G residue 408 HIS Chi-restraints excluded: chain G residue 437 SER Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 672 THR Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 323 optimal weight: 0.0050 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 237 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080674 restraints weight = 54090.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081928 restraints weight = 36303.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082558 restraints weight = 27317.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082961 restraints weight = 24855.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083127 restraints weight = 23065.718| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27824 Z= 0.103 Angle : 0.520 11.080 37527 Z= 0.250 Chirality : 0.042 0.259 4315 Planarity : 0.004 0.049 4755 Dihedral : 8.090 104.401 3980 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.30 % Allowed : 16.91 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3390 helix: 1.92 (0.13), residues: 1695 sheet: 0.01 (0.25), residues: 445 loop : 0.01 (0.19), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 303 TYR 0.017 0.001 TYR E 499 PHE 0.018 0.001 PHE G 240 TRP 0.005 0.001 TRP F 704 HIS 0.003 0.000 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00242 (27824) covalent geometry : angle 0.51956 (37527) hydrogen bonds : bond 0.03250 ( 1166) hydrogen bonds : angle 3.23293 ( 3378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.55 seconds wall clock time: 57 minutes 8.55 seconds (3428.55 seconds total)