Starting phenix.real_space_refine on Fri Nov 21 03:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ri9_53990/11_2025/9ri9_53990.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 18 5.49 5 S 180 5.16 5 C 26616 2.51 5 N 7254 2.21 5 O 7818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41886 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6950 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 829} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, G, I, J, L Time building chain proxies: 8.25, per 1000 atoms: 0.20 Number of scatterers: 41886 At special positions: 0 Unit cell: (182.988, 194.58, 110.952, 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 180 16.00 P 18 15.00 O 7818 8.00 N 7254 7.00 C 26616 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: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9852 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 36 sheets defined 50.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.819A pdb=" N LEU B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 86 Processing helix chain 'B' and resid 88 through 125 removed outlier: 4.029A pdb=" N PHE B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N TRP B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.694A pdb=" N LYS B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.569A pdb=" N TYR B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 239 " --> pdb=" O LYS B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 239' Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.721A pdb=" N TRP B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 332 through 346 removed outlier: 4.681A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 349 through 362 removed outlier: 3.890A pdb=" N GLY B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.666A pdb=" N ARG B 384 " --> pdb=" O HIS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.909A pdb=" N SER B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 removed outlier: 4.329A pdb=" N ALA B 406 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 551 through 555 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.505A pdb=" N LEU B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 676 through 682 removed outlier: 3.562A pdb=" N PHE B 680 " --> pdb=" O THR B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 700 removed outlier: 3.837A pdb=" N LEU B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.574A pdb=" N LEU B 766 " --> pdb=" O ASP B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 853 through 873 Processing helix chain 'D' and resid 21 through 50 removed outlier: 3.820A pdb=" N LEU D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 30 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 86 Processing helix chain 'D' and resid 88 through 125 removed outlier: 4.029A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N TRP D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'D' and resid 188 through 198 Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.693A pdb=" N LYS D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.570A pdb=" N TYR D 238 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 239 " --> pdb=" O LYS D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 239' Processing helix chain 'D' and resid 242 through 256 Processing helix chain 'D' and resid 269 through 277 removed outlier: 3.720A pdb=" N TRP D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'D' and resid 332 through 346 removed outlier: 4.680A pdb=" N LEU D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 349 through 362 removed outlier: 3.891A pdb=" N GLY D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.664A pdb=" N ARG D 384 " --> pdb=" O HIS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 3.908A pdb=" N SER D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D 399 " --> pdb=" O MET D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 411 removed outlier: 4.328A pdb=" N ALA D 406 " --> pdb=" O TYR D 402 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 411 " --> pdb=" O CYS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 477 through 491 Processing helix chain 'D' and resid 508 through 513 Processing helix chain 'D' and resid 523 through 529 Processing helix chain 'D' and resid 551 through 555 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.506A pdb=" N LEU D 585 " --> pdb=" O PHE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 628 through 632 Processing helix chain 'D' and resid 652 through 656 Processing helix chain 'D' and resid 671 through 675 Processing helix chain 'D' and resid 676 through 682 removed outlier: 3.563A pdb=" N PHE D 680 " --> pdb=" O THR D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 700 removed outlier: 3.835A pdb=" N LEU D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 717 Processing helix chain 'D' and resid 740 through 744 Processing helix chain 'D' and resid 762 through 767 removed outlier: 3.573A pdb=" N LEU D 766 " --> pdb=" O ASP D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 Processing helix chain 'D' and resid 853 through 873 Processing helix chain 'G' and resid 21 through 50 removed outlier: 3.818A pdb=" N LEU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 30 " --> pdb=" O GLY G 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 86 Processing helix chain 'G' and resid 88 through 125 removed outlier: 4.028A pdb=" N PHE G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N TRP G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE G 96 " --> pdb=" O PHE G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 171 Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 199 through 206 Processing helix chain 'G' and resid 219 through 230 removed outlier: 3.693A pdb=" N LYS G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 239 removed outlier: 3.569A pdb=" N TYR G 238 " --> pdb=" O THR G 235 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP G 239 " --> pdb=" O LYS G 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 235 through 239' Processing helix chain 'G' and resid 242 through 256 Processing helix chain 'G' and resid 269 through 277 removed outlier: 3.719A pdb=" N TRP G 273 " --> pdb=" O THR G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'G' and resid 332 through 346 removed outlier: 4.681A pdb=" N LEU G 337 " --> pdb=" O PRO G 333 " (cutoff:3.500A) Proline residue: G 338 - end of helix Processing helix chain 'G' and resid 349 through 362 removed outlier: 3.889A pdb=" N GLY G 362 " --> pdb=" O GLY G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 376 Processing helix chain 'G' and resid 376 through 384 removed outlier: 3.666A pdb=" N ARG G 384 " --> pdb=" O HIS G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 399 removed outlier: 3.909A pdb=" N SER G 396 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG G 399 " --> pdb=" O MET G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 411 removed outlier: 4.329A pdb=" N ALA G 406 " --> pdb=" O TYR G 402 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS G 411 " --> pdb=" O CYS G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 432 Processing helix chain 'G' and resid 442 through 457 Processing helix chain 'G' and resid 477 through 491 Processing helix chain 'G' and resid 508 through 513 Processing helix chain 'G' and resid 523 through 529 Processing helix chain 'G' and resid 551 through 555 Processing helix chain 'G' and resid 556 through 562 Processing helix chain 'G' and resid 579 through 585 removed outlier: 3.505A pdb=" N LEU G 585 " --> pdb=" O PHE G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 608 Processing helix chain 'G' and resid 628 through 632 Processing helix chain 'G' and resid 652 through 656 Processing helix chain 'G' and resid 671 through 675 Processing helix chain 'G' and resid 676 through 682 removed outlier: 3.563A pdb=" N PHE G 680 " --> pdb=" O THR G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 694 through 700 removed outlier: 3.835A pdb=" N LEU G 698 " --> pdb=" O LYS G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 717 Processing helix chain 'G' and resid 740 through 744 Processing helix chain 'G' and resid 762 through 767 removed outlier: 3.573A pdb=" N LEU G 766 " --> pdb=" O ASP G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 841 Processing helix chain 'G' and resid 853 through 873 Processing helix chain 'I' and resid 21 through 50 removed outlier: 3.818A pdb=" N LEU I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU I 30 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR I 40 " --> pdb=" O THR I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 86 Processing helix chain 'I' and resid 88 through 125 removed outlier: 4.028A pdb=" N PHE I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N TRP I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE I 96 " --> pdb=" O PHE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU I 129 " --> pdb=" O ASP I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'I' and resid 188 through 198 Processing helix chain 'I' and resid 199 through 206 Processing helix chain 'I' and resid 219 through 230 removed outlier: 3.693A pdb=" N LYS I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 239 removed outlier: 3.569A pdb=" N TYR I 238 " --> pdb=" O THR I 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP I 239 " --> pdb=" O LYS I 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 235 through 239' Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 269 through 277 removed outlier: 3.720A pdb=" N TRP I 273 " --> pdb=" O THR I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 280 No H-bonds generated for 'chain 'I' and resid 278 through 280' Processing helix chain 'I' and resid 295 through 303 Processing helix chain 'I' and resid 313 through 327 Processing helix chain 'I' and resid 332 through 346 removed outlier: 4.679A pdb=" N LEU I 337 " --> pdb=" O PRO I 333 " (cutoff:3.500A) Proline residue: I 338 - end of helix Processing helix chain 'I' and resid 349 through 362 removed outlier: 3.890A pdb=" N GLY I 362 " --> pdb=" O GLY I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 376 Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.666A pdb=" N ARG I 384 " --> pdb=" O HIS I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 399 removed outlier: 3.909A pdb=" N SER I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG I 399 " --> pdb=" O MET I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 411 removed outlier: 4.329A pdb=" N ALA I 406 " --> pdb=" O TYR I 402 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS I 407 " --> pdb=" O ASP I 403 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS I 411 " --> pdb=" O CYS I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 432 Processing helix chain 'I' and resid 442 through 457 Processing helix chain 'I' and resid 477 through 491 Processing helix chain 'I' and resid 508 through 513 Processing helix chain 'I' and resid 523 through 529 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 556 through 562 Processing helix chain 'I' and resid 579 through 585 removed outlier: 3.506A pdb=" N LEU I 585 " --> pdb=" O PHE I 582 " (cutoff:3.500A) Processing helix chain 'I' and resid 602 through 608 Processing helix chain 'I' and resid 628 through 632 Processing helix chain 'I' and resid 652 through 656 Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'I' and resid 676 through 682 removed outlier: 3.562A pdb=" N PHE I 680 " --> pdb=" O THR I 676 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 700 removed outlier: 3.836A pdb=" N LEU I 698 " --> pdb=" O LYS I 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 717 Processing helix chain 'I' and resid 740 through 744 Processing helix chain 'I' and resid 762 through 767 removed outlier: 3.574A pdb=" N LEU I 766 " --> pdb=" O ASP I 762 " (cutoff:3.500A) Processing helix chain 'I' and resid 835 through 841 Processing helix chain 'I' and resid 853 through 873 Processing helix chain 'J' and resid 21 through 50 removed outlier: 3.819A pdb=" N LEU J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 40 " --> pdb=" O THR J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 86 Processing helix chain 'J' and resid 88 through 125 removed outlier: 4.028A pdb=" N PHE J 92 " --> pdb=" O ASP J 88 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N TRP J 95 " --> pdb=" O LYS J 91 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE J 96 " --> pdb=" O PHE J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU J 129 " --> pdb=" O ASP J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'J' and resid 188 through 198 Processing helix chain 'J' and resid 199 through 206 Processing helix chain 'J' and resid 219 through 230 removed outlier: 3.693A pdb=" N LYS J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 239 removed outlier: 3.569A pdb=" N TYR J 238 " --> pdb=" O THR J 235 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP J 239 " --> pdb=" O LYS J 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 235 through 239' Processing helix chain 'J' and resid 242 through 256 Processing helix chain 'J' and resid 269 through 277 removed outlier: 3.719A pdb=" N TRP J 273 " --> pdb=" O THR J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 280 No H-bonds generated for 'chain 'J' and resid 278 through 280' Processing helix chain 'J' and resid 295 through 303 Processing helix chain 'J' and resid 313 through 327 Processing helix chain 'J' and resid 332 through 346 removed outlier: 4.681A pdb=" N LEU J 337 " --> pdb=" O PRO J 333 " (cutoff:3.500A) Proline residue: J 338 - end of helix Processing helix chain 'J' and resid 349 through 362 removed outlier: 3.890A pdb=" N GLY J 362 " --> pdb=" O GLY J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 376 Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.667A pdb=" N ARG J 384 " --> pdb=" O HIS J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 399 removed outlier: 3.908A pdb=" N SER J 396 " --> pdb=" O LEU J 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG J 399 " --> pdb=" O MET J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 411 removed outlier: 4.328A pdb=" N ALA J 406 " --> pdb=" O TYR J 402 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS J 407 " --> pdb=" O ASP J 403 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS J 411 " --> pdb=" O CYS J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 432 Processing helix chain 'J' and resid 442 through 457 Processing helix chain 'J' and resid 477 through 491 Processing helix chain 'J' and resid 508 through 513 Processing helix chain 'J' and resid 523 through 529 Processing helix chain 'J' and resid 551 through 555 Processing helix chain 'J' and resid 556 through 562 Processing helix chain 'J' and resid 579 through 585 removed outlier: 3.506A pdb=" N LEU J 585 " --> pdb=" O PHE J 582 " (cutoff:3.500A) Processing helix chain 'J' and resid 602 through 608 Processing helix chain 'J' and resid 628 through 632 Processing helix chain 'J' and resid 652 through 656 Processing helix chain 'J' and resid 671 through 675 Processing helix chain 'J' and resid 676 through 682 removed outlier: 3.563A pdb=" N PHE J 680 " --> pdb=" O THR J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 694 through 700 removed outlier: 3.835A pdb=" N LEU J 698 " --> pdb=" O LYS J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 717 Processing helix chain 'J' and resid 740 through 744 Processing helix chain 'J' and resid 762 through 767 removed outlier: 3.573A pdb=" N LEU J 766 " --> pdb=" O ASP J 762 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 841 Processing helix chain 'J' and resid 853 through 873 Processing helix chain 'L' and resid 21 through 50 removed outlier: 3.819A pdb=" N LEU L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN L 33 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 40 " --> pdb=" O THR L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 86 Processing helix chain 'L' and resid 88 through 125 removed outlier: 4.029A pdb=" N PHE L 92 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N TRP L 95 " --> pdb=" O LYS L 91 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE L 96 " --> pdb=" O PHE L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 135 removed outlier: 3.566A pdb=" N LEU L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'L' and resid 188 through 198 Processing helix chain 'L' and resid 199 through 206 Processing helix chain 'L' and resid 219 through 230 removed outlier: 3.693A pdb=" N LYS L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 239 removed outlier: 3.569A pdb=" N TYR L 238 " --> pdb=" O THR L 235 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP L 239 " --> pdb=" O LYS L 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 235 through 239' Processing helix chain 'L' and resid 242 through 256 Processing helix chain 'L' and resid 269 through 277 removed outlier: 3.720A pdb=" N TRP L 273 " --> pdb=" O THR L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 280 No H-bonds generated for 'chain 'L' and resid 278 through 280' Processing helix chain 'L' and resid 295 through 303 Processing helix chain 'L' and resid 313 through 327 Processing helix chain 'L' and resid 332 through 346 removed outlier: 4.680A pdb=" N LEU L 337 " --> pdb=" O PRO L 333 " (cutoff:3.500A) Proline residue: L 338 - end of helix Processing helix chain 'L' and resid 349 through 362 removed outlier: 3.889A pdb=" N GLY L 362 " --> pdb=" O GLY L 358 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 376 Processing helix chain 'L' and resid 376 through 384 removed outlier: 3.666A pdb=" N ARG L 384 " --> pdb=" O HIS L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 399 removed outlier: 3.909A pdb=" N SER L 396 " --> pdb=" O LEU L 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG L 399 " --> pdb=" O MET L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 411 removed outlier: 4.328A pdb=" N ALA L 406 " --> pdb=" O TYR L 402 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS L 407 " --> pdb=" O ASP L 403 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS L 411 " --> pdb=" O CYS L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 432 Processing helix chain 'L' and resid 442 through 457 Processing helix chain 'L' and resid 477 through 491 Processing helix chain 'L' and resid 508 through 513 Processing helix chain 'L' and resid 523 through 529 Processing helix chain 'L' and resid 551 through 555 Processing helix chain 'L' and resid 556 through 562 Processing helix chain 'L' and resid 579 through 585 removed outlier: 3.506A pdb=" N LEU L 585 " --> pdb=" O PHE L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 602 through 608 Processing helix chain 'L' and resid 628 through 632 Processing helix chain 'L' and resid 652 through 656 Processing helix chain 'L' and resid 671 through 675 Processing helix chain 'L' and resid 676 through 682 removed outlier: 3.563A pdb=" N PHE L 680 " --> pdb=" O THR L 676 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 700 removed outlier: 3.836A pdb=" N LEU L 698 " --> pdb=" O LYS L 694 " (cutoff:3.500A) Processing helix chain 'L' and resid 709 through 717 Processing helix chain 'L' and resid 740 through 744 Processing helix chain 'L' and resid 762 through 767 removed outlier: 3.575A pdb=" N LEU L 766 " --> pdb=" O ASP L 762 " (cutoff:3.500A) Processing helix chain 'L' and resid 835 through 841 Processing helix chain 'L' and resid 853 through 873 Processing sheet with id=AA1, first strand: chain 'B' and resid 208 through 213 removed outlier: 6.017A pdb=" N TYR B 260 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 290 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 262 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR B 292 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 264 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B 177 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET B 291 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 179 " --> pdb=" O MET B 291 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR B 293 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 181 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 420 through 421 removed outlier: 6.845A pdb=" N ILE B 471 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG B 465 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 473 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 496 through 498 removed outlier: 5.248A pdb=" N GLU B 571 " --> pdb=" O CYS B 542 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 548 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 498 removed outlier: 5.248A pdb=" N GLU B 571 " --> pdb=" O CYS B 542 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER B 594 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER B 572 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE B 591 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLU B 617 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 593 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL B 638 " --> pdb=" O SER B 668 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 670 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 667 " --> pdb=" O GLY B 690 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG B 692 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR B 669 " --> pdb=" O ARG B 692 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 689 " --> pdb=" O LYS B 724 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL B 726 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 691 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 723 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL B 754 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 725 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 824 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 823 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN B 850 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 825 " --> pdb=" O GLN B 850 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE B 847 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE B 885 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 849 " --> pdb=" O PHE B 885 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 600 through 601 Processing sheet with id=AA6, first strand: chain 'B' and resid 758 through 759 removed outlier: 6.197A pdb=" N PHE B 758 " --> pdb=" O LYS B 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 208 through 213 removed outlier: 6.017A pdb=" N TYR D 260 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 290 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 262 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR D 292 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU D 264 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 420 through 421 removed outlier: 6.844A pdb=" N ILE D 471 " --> pdb=" O ARG D 465 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG D 465 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 473 " --> pdb=" O THR D 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU D 571 " --> pdb=" O CYS D 542 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 548 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU D 571 " --> pdb=" O CYS D 542 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 594 " --> pdb=" O ALA D 570 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER D 572 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE D 591 " --> pdb=" O ILE D 615 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLU D 617 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU D 593 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL D 638 " --> pdb=" O SER D 668 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 670 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 667 " --> pdb=" O GLY D 690 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG D 692 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR D 669 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 689 " --> pdb=" O LYS D 724 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL D 726 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 691 " --> pdb=" O VAL D 726 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 723 " --> pdb=" O SER D 752 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL D 754 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 725 " --> pdb=" O VAL D 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 824 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 823 " --> pdb=" O GLU D 848 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN D 850 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU D 825 " --> pdb=" O GLN D 850 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE D 847 " --> pdb=" O SER D 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE D 885 " --> pdb=" O ILE D 847 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 849 " --> pdb=" O PHE D 885 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 600 through 601 Processing sheet with id=AB3, first strand: chain 'D' and resid 758 through 759 removed outlier: 6.198A pdb=" N PHE D 758 " --> pdb=" O LYS D 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 208 through 213 removed outlier: 6.017A pdb=" N TYR G 260 " --> pdb=" O ARG G 288 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU G 290 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE G 262 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR G 292 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 264 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU G 177 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET G 291 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL G 179 " --> pdb=" O MET G 291 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR G 293 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL G 181 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 420 through 421 removed outlier: 6.845A pdb=" N ILE G 471 " --> pdb=" O ARG G 465 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG G 465 " --> pdb=" O ILE G 471 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR G 473 " --> pdb=" O THR G 463 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU G 571 " --> pdb=" O CYS G 542 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE G 548 " --> pdb=" O LYS G 574 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU G 571 " --> pdb=" O CYS G 542 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER G 594 " --> pdb=" O ALA G 570 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER G 572 " --> pdb=" O SER G 594 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE G 591 " --> pdb=" O ILE G 615 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU G 617 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 593 " --> pdb=" O GLU G 617 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL G 638 " --> pdb=" O SER G 668 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE G 670 " --> pdb=" O VAL G 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 667 " --> pdb=" O GLY G 690 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG G 692 " --> pdb=" O LEU G 667 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR G 669 " --> pdb=" O ARG G 692 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU G 689 " --> pdb=" O LYS G 724 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL G 726 " --> pdb=" O LEU G 689 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL G 691 " --> pdb=" O VAL G 726 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU G 723 " --> pdb=" O SER G 752 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL G 754 " --> pdb=" O LEU G 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU G 725 " --> pdb=" O VAL G 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 824 " --> pdb=" O LEU G 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 823 " --> pdb=" O GLU G 848 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN G 850 " --> pdb=" O LEU G 823 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU G 825 " --> pdb=" O GLN G 850 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE G 847 " --> pdb=" O SER G 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE G 885 " --> pdb=" O ILE G 847 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU G 849 " --> pdb=" O PHE G 885 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 600 through 601 Processing sheet with id=AB9, first strand: chain 'G' and resid 758 through 759 removed outlier: 6.198A pdb=" N PHE G 758 " --> pdb=" O LYS G 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 208 through 213 removed outlier: 6.017A pdb=" N TYR I 260 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU I 290 " --> pdb=" O TYR I 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE I 262 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR I 292 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU I 264 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU I 177 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET I 291 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL I 179 " --> pdb=" O MET I 291 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR I 293 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL I 181 " --> pdb=" O THR I 293 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 420 through 421 removed outlier: 6.844A pdb=" N ILE I 471 " --> pdb=" O ARG I 465 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG I 465 " --> pdb=" O ILE I 471 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR I 473 " --> pdb=" O THR I 463 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU I 571 " --> pdb=" O CYS I 542 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE I 548 " --> pdb=" O LYS I 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU I 571 " --> pdb=" O CYS I 542 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER I 594 " --> pdb=" O ALA I 570 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER I 572 " --> pdb=" O SER I 594 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE I 591 " --> pdb=" O ILE I 615 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU I 617 " --> pdb=" O ILE I 591 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU I 593 " --> pdb=" O GLU I 617 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL I 638 " --> pdb=" O SER I 668 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE I 670 " --> pdb=" O VAL I 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU I 667 " --> pdb=" O GLY I 690 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ARG I 692 " --> pdb=" O LEU I 667 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR I 669 " --> pdb=" O ARG I 692 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU I 689 " --> pdb=" O LYS I 724 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL I 726 " --> pdb=" O LEU I 689 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL I 691 " --> pdb=" O VAL I 726 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU I 723 " --> pdb=" O SER I 752 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL I 754 " --> pdb=" O LEU I 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU I 725 " --> pdb=" O VAL I 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA I 824 " --> pdb=" O LEU I 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU I 823 " --> pdb=" O GLU I 848 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN I 850 " --> pdb=" O LEU I 823 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU I 825 " --> pdb=" O GLN I 850 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE I 847 " --> pdb=" O SER I 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE I 885 " --> pdb=" O ILE I 847 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 849 " --> pdb=" O PHE I 885 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 600 through 601 Processing sheet with id=AC6, first strand: chain 'I' and resid 758 through 759 removed outlier: 6.198A pdb=" N PHE I 758 " --> pdb=" O LYS I 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 208 through 213 removed outlier: 6.017A pdb=" N TYR J 260 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU J 290 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE J 262 " --> pdb=" O LEU J 290 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR J 292 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU J 264 " --> pdb=" O THR J 292 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU J 177 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET J 291 " --> pdb=" O GLU J 177 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL J 179 " --> pdb=" O MET J 291 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR J 293 " --> pdb=" O VAL J 179 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL J 181 " --> pdb=" O THR J 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 420 through 421 removed outlier: 6.845A pdb=" N ILE J 471 " --> pdb=" O ARG J 465 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG J 465 " --> pdb=" O ILE J 471 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR J 473 " --> pdb=" O THR J 463 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 496 through 498 removed outlier: 5.250A pdb=" N GLU J 571 " --> pdb=" O CYS J 542 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE J 548 " --> pdb=" O LYS J 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 496 through 498 removed outlier: 5.250A pdb=" N GLU J 571 " --> pdb=" O CYS J 542 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER J 594 " --> pdb=" O ALA J 570 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER J 572 " --> pdb=" O SER J 594 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE J 591 " --> pdb=" O ILE J 615 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU J 617 " --> pdb=" O ILE J 591 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 593 " --> pdb=" O GLU J 617 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL J 638 " --> pdb=" O SER J 668 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE J 670 " --> pdb=" O VAL J 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU J 667 " --> pdb=" O GLY J 690 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG J 692 " --> pdb=" O LEU J 667 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR J 669 " --> pdb=" O ARG J 692 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU J 689 " --> pdb=" O LYS J 724 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL J 726 " --> pdb=" O LEU J 689 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL J 691 " --> pdb=" O VAL J 726 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU J 723 " --> pdb=" O SER J 752 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL J 754 " --> pdb=" O LEU J 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU J 725 " --> pdb=" O VAL J 754 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA J 824 " --> pdb=" O LEU J 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU J 823 " --> pdb=" O GLU J 848 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLN J 850 " --> pdb=" O LEU J 823 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU J 825 " --> pdb=" O GLN J 850 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE J 847 " --> pdb=" O SER J 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE J 885 " --> pdb=" O ILE J 847 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU J 849 " --> pdb=" O PHE J 885 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 600 through 601 Processing sheet with id=AD3, first strand: chain 'J' and resid 758 through 759 removed outlier: 6.198A pdb=" N PHE J 758 " --> pdb=" O LYS J 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L' and resid 208 through 213 removed outlier: 6.016A pdb=" N TYR L 260 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU L 290 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE L 262 " --> pdb=" O LEU L 290 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR L 292 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU L 264 " --> pdb=" O THR L 292 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU L 177 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET L 291 " --> pdb=" O GLU L 177 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL L 179 " --> pdb=" O MET L 291 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR L 293 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL L 181 " --> pdb=" O THR L 293 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 420 through 421 removed outlier: 6.845A pdb=" N ILE L 471 " --> pdb=" O ARG L 465 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG L 465 " --> pdb=" O ILE L 471 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR L 473 " --> pdb=" O THR L 463 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU L 571 " --> pdb=" O CYS L 542 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE L 548 " --> pdb=" O LYS L 574 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 496 through 498 removed outlier: 5.249A pdb=" N GLU L 571 " --> pdb=" O CYS L 542 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER L 594 " --> pdb=" O ALA L 570 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER L 572 " --> pdb=" O SER L 594 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE L 591 " --> pdb=" O ILE L 615 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU L 617 " --> pdb=" O ILE L 591 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU L 593 " --> pdb=" O GLU L 617 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL L 638 " --> pdb=" O SER L 668 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE L 670 " --> pdb=" O VAL L 638 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU L 667 " --> pdb=" O GLY L 690 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG L 692 " --> pdb=" O LEU L 667 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR L 669 " --> pdb=" O ARG L 692 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU L 689 " --> pdb=" O LYS L 724 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL L 726 " --> pdb=" O LEU L 689 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL L 691 " --> pdb=" O VAL L 726 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU L 723 " --> pdb=" O SER L 752 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL L 754 " --> pdb=" O LEU L 723 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU L 725 " --> pdb=" O VAL L 754 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 824 " --> pdb=" O LEU L 800 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU L 823 " --> pdb=" O GLU L 848 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN L 850 " --> pdb=" O LEU L 823 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU L 825 " --> pdb=" O GLN L 850 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE L 847 " --> pdb=" O SER L 883 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE L 885 " --> pdb=" O ILE L 847 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU L 849 " --> pdb=" O PHE L 885 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 600 through 601 Processing sheet with id=AD9, first strand: chain 'L' and resid 758 through 759 removed outlier: 6.198A pdb=" N PHE L 758 " --> pdb=" O LYS L 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 1907 hydrogen bonds defined for protein. 5145 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: 13.83 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13788 1.34 - 1.46: 8456 1.46 - 1.58: 20184 1.58 - 1.70: 22 1.70 - 1.81: 258 Bond restraints: 42708 Sorted by residual: bond pdb=" N VAL G 537 " pdb=" CA VAL G 537 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.34e+00 bond pdb=" N VAL L 537 " pdb=" CA VAL L 537 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.30e+00 bond pdb=" N VAL D 537 " pdb=" CA VAL D 537 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.30e+00 bond pdb=" N VAL B 537 " pdb=" CA VAL B 537 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.28e+00 bond pdb=" N VAL I 537 " pdb=" CA VAL I 537 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 9.10e+00 ... (remaining 42703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 56679 1.79 - 3.58: 727 3.58 - 5.37: 182 5.37 - 7.15: 42 7.15 - 8.94: 36 Bond angle restraints: 57666 Sorted by residual: angle pdb=" C LEU J 381 " pdb=" N ILE J 382 " pdb=" CA ILE J 382 " ideal model delta sigma weight residual 123.16 117.68 5.48 1.06e+00 8.90e-01 2.67e+01 angle pdb=" C LEU D 381 " pdb=" N ILE D 382 " pdb=" CA ILE D 382 " ideal model delta sigma weight residual 123.16 117.68 5.48 1.06e+00 8.90e-01 2.67e+01 angle pdb=" C LEU L 381 " pdb=" N ILE L 382 " pdb=" CA ILE L 382 " ideal model delta sigma weight residual 123.16 117.70 5.46 1.06e+00 8.90e-01 2.65e+01 angle pdb=" C LEU B 381 " pdb=" N ILE B 382 " pdb=" CA ILE B 382 " ideal model delta sigma weight residual 123.16 117.71 5.45 1.06e+00 8.90e-01 2.65e+01 angle pdb=" C LEU I 381 " pdb=" N ILE I 382 " pdb=" CA ILE I 382 " ideal model delta sigma weight residual 123.16 117.71 5.45 1.06e+00 8.90e-01 2.64e+01 ... (remaining 57661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 23564 17.52 - 35.04: 2122 35.04 - 52.56: 552 52.56 - 70.08: 30 70.08 - 87.59: 54 Dihedral angle restraints: 26322 sinusoidal: 11172 harmonic: 15150 Sorted by residual: dihedral pdb=" CD ARG B 516 " pdb=" NE ARG B 516 " pdb=" CZ ARG B 516 " pdb=" NH1 ARG B 516 " ideal model delta sinusoidal sigma weight residual 0.00 36.10 -36.10 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CD ARG G 516 " pdb=" NE ARG G 516 " pdb=" CZ ARG G 516 " pdb=" NH1 ARG G 516 " ideal model delta sinusoidal sigma weight residual 0.00 36.08 -36.08 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CD ARG D 516 " pdb=" NE ARG D 516 " pdb=" CZ ARG D 516 " pdb=" NH1 ARG D 516 " ideal model delta sinusoidal sigma weight residual 0.00 35.99 -35.99 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 26319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 4039 0.030 - 0.060: 1543 0.060 - 0.091: 466 0.091 - 0.121: 286 0.121 - 0.151: 86 Chirality restraints: 6420 Sorted by residual: chirality pdb=" CA GLU J 379 " pdb=" N GLU J 379 " pdb=" C GLU J 379 " pdb=" CB GLU J 379 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA GLU B 379 " pdb=" N GLU B 379 " pdb=" C GLU B 379 " pdb=" CB GLU B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA GLU D 379 " pdb=" N GLU D 379 " pdb=" C GLU D 379 " pdb=" CB GLU D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 6417 not shown) Planarity restraints: 7374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 516 " -0.642 9.50e-02 1.11e+02 2.88e-01 5.05e+01 pdb=" NE ARG G 516 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG G 516 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 516 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 516 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 516 " 0.641 9.50e-02 1.11e+02 2.87e-01 5.04e+01 pdb=" NE ARG B 516 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 516 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 516 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 516 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 516 " -0.641 9.50e-02 1.11e+02 2.87e-01 5.04e+01 pdb=" NE ARG J 516 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG J 516 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 516 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 516 " -0.021 2.00e-02 2.50e+03 ... (remaining 7371 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7461 2.78 - 3.31: 40300 3.31 - 3.84: 66857 3.84 - 4.37: 81663 4.37 - 4.90: 138373 Nonbonded interactions: 334654 Sorted by model distance: nonbonded pdb=" NH2 ARG J 294 " pdb=" O3G ATP J1001 " model vdw 2.246 3.120 nonbonded pdb=" NH2 ARG L 294 " pdb=" O3G ATP L1001 " model vdw 2.246 3.120 nonbonded pdb=" NH2 ARG G 294 " pdb=" O3G ATP G1001 " model vdw 2.246 3.120 nonbonded pdb=" NH2 ARG I 294 " pdb=" O3G ATP I1001 " model vdw 2.247 3.120 nonbonded pdb=" NH2 ARG D 294 " pdb=" O3G ATP D1001 " model vdw 2.247 3.120 ... (remaining 334649 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.540 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 42.850 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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 : 0.003 0.046 42708 Z= 0.164 Angle : 0.577 8.943 57666 Z= 0.306 Chirality : 0.041 0.151 6420 Planarity : 0.010 0.288 7374 Dihedral : 14.323 87.595 16470 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.39 % Allowed : 12.06 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.09 (0.12), residues: 5184 helix: 1.06 (0.11), residues: 2316 sheet: -0.19 (0.20), residues: 708 loop : 0.93 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 580 TYR 0.013 0.001 TYR L 260 PHE 0.015 0.001 PHE G 758 TRP 0.027 0.001 TRP L 757 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00280 (42708) covalent geometry : angle 0.57688 (57666) hydrogen bonds : bond 0.15384 ( 1859) hydrogen bonds : angle 7.02775 ( 5145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8616 (mp0) REVERT: B 110 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8554 (tt0) REVERT: B 461 MET cc_start: 0.9050 (mtp) cc_final: 0.8848 (mtm) REVERT: B 580 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8057 (ttp-110) REVERT: B 747 LYS cc_start: 0.8394 (mttt) cc_final: 0.8108 (mtpt) REVERT: B 758 PHE cc_start: 0.8616 (m-80) cc_final: 0.8354 (m-10) REVERT: D 73 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8568 (mp0) REVERT: D 110 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8517 (tt0) REVERT: D 391 LYS cc_start: 0.8989 (mtpm) cc_final: 0.8480 (mptt) REVERT: D 399 ARG cc_start: 0.8614 (ttt90) cc_final: 0.8352 (mtt90) REVERT: D 580 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8042 (ttp-110) REVERT: D 747 LYS cc_start: 0.8541 (mttt) cc_final: 0.8242 (mtpt) REVERT: D 758 PHE cc_start: 0.8682 (m-80) cc_final: 0.8368 (m-10) REVERT: G 110 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8552 (tt0) REVERT: G 391 LYS cc_start: 0.8986 (mtpm) cc_final: 0.8519 (mptt) REVERT: G 580 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8010 (ttp-110) REVERT: G 747 LYS cc_start: 0.8392 (mttt) cc_final: 0.8171 (mtpt) REVERT: I 110 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8540 (tt0) REVERT: I 391 LYS cc_start: 0.8982 (mtpm) cc_final: 0.8520 (mptt) REVERT: I 580 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8026 (ttp-110) REVERT: I 747 LYS cc_start: 0.8450 (mttt) cc_final: 0.8220 (mtpt) REVERT: J 73 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8612 (mp0) REVERT: J 110 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8551 (tt0) REVERT: J 461 MET cc_start: 0.9053 (mtp) cc_final: 0.8848 (mtm) REVERT: J 580 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8054 (ttp-110) REVERT: J 758 PHE cc_start: 0.8631 (m-80) cc_final: 0.8357 (m-10) REVERT: L 73 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8570 (mp0) REVERT: L 110 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8526 (tt0) REVERT: L 391 LYS cc_start: 0.8984 (mtpm) cc_final: 0.8471 (mptt) REVERT: L 399 ARG cc_start: 0.8606 (ttt90) cc_final: 0.8339 (mtt90) REVERT: L 580 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8070 (ttp-110) REVERT: L 747 LYS cc_start: 0.8555 (mttt) cc_final: 0.8258 (mtpt) REVERT: L 758 PHE cc_start: 0.8623 (m-80) cc_final: 0.8336 (m-10) outliers start: 18 outliers final: 5 residues processed: 262 average time/residue: 0.8818 time to fit residues: 275.6790 Evaluate side-chains 225 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 220 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN B 481 HIS B 816 ASN D 394 GLN D 481 HIS D 816 ASN G 394 GLN G 481 HIS G 816 ASN I 394 GLN I 481 HIS I 816 ASN J 394 GLN J 481 HIS J 816 ASN L 394 GLN L 481 HIS L 816 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.068433 restraints weight = 77172.091| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.92 r_work: 0.2727 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 42708 Z= 0.287 Angle : 0.594 8.021 57666 Z= 0.302 Chirality : 0.044 0.157 6420 Planarity : 0.005 0.041 7374 Dihedral : 7.820 88.889 5798 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.87 % Allowed : 11.69 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.07 (0.12), residues: 5184 helix: 1.00 (0.11), residues: 2334 sheet: 0.23 (0.21), residues: 672 loop : 0.79 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 538 TYR 0.020 0.002 TYR L 197 PHE 0.016 0.002 PHE G 782 TRP 0.009 0.001 TRP J 370 HIS 0.005 0.001 HIS I 307 Details of bonding type rmsd covalent geometry : bond 0.00693 (42708) covalent geometry : angle 0.59372 (57666) hydrogen bonds : bond 0.04175 ( 1859) hydrogen bonds : angle 5.10560 ( 5145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 248 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8590 (tt0) REVERT: B 747 LYS cc_start: 0.8597 (mttt) cc_final: 0.8386 (mtmt) REVERT: B 758 PHE cc_start: 0.8814 (m-80) cc_final: 0.8611 (m-10) REVERT: B 782 PHE cc_start: 0.8762 (m-10) cc_final: 0.8536 (m-80) REVERT: B 845 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7600 (mm110) REVERT: D 747 LYS cc_start: 0.8713 (mttt) cc_final: 0.8379 (mtpt) REVERT: D 845 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7515 (mm110) REVERT: G 73 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: G 110 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8592 (tt0) REVERT: G 747 LYS cc_start: 0.8583 (mttt) cc_final: 0.8072 (mmmm) REVERT: G 758 PHE cc_start: 0.8442 (m-80) cc_final: 0.8141 (m-10) REVERT: G 845 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7645 (mm110) REVERT: I 73 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: I 110 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8572 (tt0) REVERT: I 747 LYS cc_start: 0.8627 (mttt) cc_final: 0.8115 (mmmm) REVERT: I 758 PHE cc_start: 0.8326 (m-80) cc_final: 0.8034 (m-10) REVERT: I 845 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7616 (mm110) REVERT: J 110 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8615 (tt0) REVERT: J 127 TYR cc_start: 0.9068 (m-80) cc_final: 0.8859 (m-80) REVERT: J 845 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (mm110) REVERT: L 130 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8579 (mm110) REVERT: L 747 LYS cc_start: 0.8704 (mttt) cc_final: 0.8375 (mtpt) REVERT: L 845 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7519 (mm110) outliers start: 86 outliers final: 26 residues processed: 316 average time/residue: 0.9319 time to fit residues: 347.3416 Evaluate side-chains 249 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 633 THR Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 633 THR Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 73 optimal weight: 9.9990 chunk 451 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 426 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 483 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070500 restraints weight = 76910.918| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.93 r_work: 0.2764 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42708 Z= 0.127 Angle : 0.479 7.572 57666 Z= 0.242 Chirality : 0.040 0.147 6420 Planarity : 0.003 0.038 7374 Dihedral : 7.617 89.766 5796 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.24 % Allowed : 12.91 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.29 (0.12), residues: 5184 helix: 1.22 (0.11), residues: 2334 sheet: 0.04 (0.20), residues: 726 loop : 0.99 (0.15), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 538 TYR 0.011 0.001 TYR I 197 PHE 0.011 0.001 PHE J 758 TRP 0.013 0.001 TRP B 787 HIS 0.003 0.001 HIS J 97 Details of bonding type rmsd covalent geometry : bond 0.00297 (42708) covalent geometry : angle 0.47881 (57666) hydrogen bonds : bond 0.03504 ( 1859) hydrogen bonds : angle 4.80910 ( 5145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8581 (tt0) REVERT: B 391 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8329 (mtmm) REVERT: B 747 LYS cc_start: 0.8483 (mttt) cc_final: 0.8033 (mmmm) REVERT: B 782 PHE cc_start: 0.8714 (m-10) cc_final: 0.8506 (m-80) REVERT: D 130 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8468 (mm110) REVERT: D 747 LYS cc_start: 0.8639 (mttt) cc_final: 0.8309 (mtpt) REVERT: G 73 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: G 110 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8541 (tt0) REVERT: G 747 LYS cc_start: 0.8578 (mttt) cc_final: 0.8078 (mmmm) REVERT: G 758 PHE cc_start: 0.8387 (m-80) cc_final: 0.8146 (m-10) REVERT: I 73 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: I 110 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8545 (tt0) REVERT: I 747 LYS cc_start: 0.8577 (mttt) cc_final: 0.8083 (mmmm) REVERT: J 110 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8564 (tt0) REVERT: J 130 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8799 (mm110) REVERT: J 391 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8319 (mtmm) REVERT: L 130 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8510 (mm-40) REVERT: L 747 LYS cc_start: 0.8639 (mttt) cc_final: 0.8308 (mtpt) outliers start: 57 outliers final: 23 residues processed: 288 average time/residue: 0.9518 time to fit residues: 323.0045 Evaluate side-chains 251 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 270 optimal weight: 0.0970 chunk 498 optimal weight: 8.9990 chunk 469 optimal weight: 0.4980 chunk 330 optimal weight: 0.9990 chunk 255 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 419 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 816 ASN G 216 GLN G 816 ASN ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 816 ASN J 130 GLN L 816 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071589 restraints weight = 76987.250| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.93 r_work: 0.2793 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 42708 Z= 0.102 Angle : 0.462 7.551 57666 Z= 0.233 Chirality : 0.039 0.151 6420 Planarity : 0.003 0.036 7374 Dihedral : 7.499 89.127 5796 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.83 % Allowed : 12.78 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.40 (0.12), residues: 5184 helix: 1.34 (0.11), residues: 2334 sheet: 0.10 (0.22), residues: 678 loop : 0.98 (0.15), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 538 TYR 0.014 0.001 TYR I 127 PHE 0.011 0.001 PHE J 782 TRP 0.015 0.001 TRP B 810 HIS 0.003 0.000 HIS J 97 Details of bonding type rmsd covalent geometry : bond 0.00237 (42708) covalent geometry : angle 0.46229 (57666) hydrogen bonds : bond 0.03092 ( 1859) hydrogen bonds : angle 4.54284 ( 5145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 251 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8542 (tt0) REVERT: B 391 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8323 (mtmm) REVERT: B 747 LYS cc_start: 0.8443 (mttt) cc_final: 0.8007 (mmmm) REVERT: B 763 MET cc_start: 0.9153 (tpp) cc_final: 0.8901 (mmm) REVERT: B 845 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7583 (mm110) REVERT: D 130 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8499 (mm110) REVERT: D 747 LYS cc_start: 0.8576 (mttt) cc_final: 0.8235 (mtpt) REVERT: D 845 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7503 (mm110) REVERT: G 110 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8510 (tt0) REVERT: G 747 LYS cc_start: 0.8493 (mttt) cc_final: 0.8008 (mmmm) REVERT: G 845 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7663 (mm110) REVERT: I 110 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8497 (tt0) REVERT: I 747 LYS cc_start: 0.8560 (mttt) cc_final: 0.8072 (mmmm) REVERT: I 845 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7602 (mm110) REVERT: J 110 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8559 (tt0) REVERT: J 130 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8773 (mm110) REVERT: J 391 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8328 (mtmm) REVERT: J 763 MET cc_start: 0.9123 (tpp) cc_final: 0.8880 (mmm) REVERT: J 845 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (mm110) REVERT: L 73 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: L 747 LYS cc_start: 0.8594 (mttt) cc_final: 0.8266 (mtpt) REVERT: L 845 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7498 (mm110) outliers start: 84 outliers final: 28 residues processed: 315 average time/residue: 0.9075 time to fit residues: 339.7787 Evaluate side-chains 268 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 73 GLU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 38 optimal weight: 0.0270 chunk 384 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 216 optimal weight: 0.0970 chunk 472 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 403 optimal weight: 0.9980 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072058 restraints weight = 76612.589| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.92 r_work: 0.2804 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42708 Z= 0.100 Angle : 0.455 7.818 57666 Z= 0.229 Chirality : 0.039 0.145 6420 Planarity : 0.003 0.039 7374 Dihedral : 7.335 85.940 5796 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.69 % Allowed : 13.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.46 (0.12), residues: 5184 helix: 1.40 (0.11), residues: 2334 sheet: 0.14 (0.22), residues: 678 loop : 1.00 (0.15), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 538 TYR 0.011 0.001 TYR G 127 PHE 0.012 0.001 PHE D 758 TRP 0.020 0.001 TRP D 810 HIS 0.003 0.000 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00228 (42708) covalent geometry : angle 0.45487 (57666) hydrogen bonds : bond 0.02983 ( 1859) hydrogen bonds : angle 4.40485 ( 5145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8541 (tt0) REVERT: B 479 MET cc_start: 0.8404 (ttm) cc_final: 0.8165 (ttm) REVERT: B 747 LYS cc_start: 0.8405 (mttt) cc_final: 0.7979 (mmmm) REVERT: B 763 MET cc_start: 0.9133 (tpp) cc_final: 0.8868 (mmm) REVERT: B 845 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7558 (mm110) REVERT: D 130 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8532 (mm110) REVERT: D 747 LYS cc_start: 0.8551 (mttt) cc_final: 0.8095 (mmmm) REVERT: D 758 PHE cc_start: 0.8621 (m-80) cc_final: 0.8406 (m-10) REVERT: D 845 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7513 (mm110) REVERT: G 73 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: G 110 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8505 (tt0) REVERT: G 233 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: G 747 LYS cc_start: 0.8424 (mttt) cc_final: 0.7946 (mmmm) REVERT: G 758 PHE cc_start: 0.8134 (m-80) cc_final: 0.7912 (m-10) REVERT: G 845 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7632 (mm110) REVERT: I 73 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: I 110 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8492 (tt0) REVERT: I 461 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: I 747 LYS cc_start: 0.8512 (mttt) cc_final: 0.8036 (mmmm) REVERT: I 758 PHE cc_start: 0.8316 (m-80) cc_final: 0.8084 (m-10) REVERT: I 763 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8814 (tpp) REVERT: I 845 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7610 (mm110) REVERT: J 110 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8532 (tt0) REVERT: J 391 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8417 (mtmm) REVERT: J 845 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7560 (mm110) REVERT: L 130 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8464 (mm110) REVERT: L 747 LYS cc_start: 0.8551 (mttt) cc_final: 0.8098 (mmmm) REVERT: L 758 PHE cc_start: 0.8610 (m-80) cc_final: 0.8393 (m-10) REVERT: L 845 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7501 (mm110) outliers start: 78 outliers final: 41 residues processed: 303 average time/residue: 0.9686 time to fit residues: 346.5859 Evaluate side-chains 272 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 823 LEU Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 461 MET Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 763 MET Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 241 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 361 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 197 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.118858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.071953 restraints weight = 77033.377| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.93 r_work: 0.2794 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 42708 Z= 0.103 Angle : 0.454 8.071 57666 Z= 0.228 Chirality : 0.039 0.141 6420 Planarity : 0.003 0.041 7374 Dihedral : 7.151 82.115 5796 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.83 % Allowed : 13.34 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.53 (0.12), residues: 5184 helix: 1.46 (0.11), residues: 2334 sheet: 0.21 (0.22), residues: 678 loop : 1.01 (0.15), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 804 TYR 0.009 0.001 TYR L 260 PHE 0.010 0.001 PHE D 782 TRP 0.021 0.001 TRP I 810 HIS 0.002 0.000 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00241 (42708) covalent geometry : angle 0.45406 (57666) hydrogen bonds : bond 0.02968 ( 1859) hydrogen bonds : angle 4.31554 ( 5145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 239 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8560 (tt0) REVERT: B 391 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8225 (mtmm) REVERT: B 747 LYS cc_start: 0.8398 (mttt) cc_final: 0.7969 (mmmm) REVERT: B 845 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7534 (mm110) REVERT: D 130 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8568 (mm110) REVERT: D 747 LYS cc_start: 0.8565 (mttt) cc_final: 0.8114 (mmmm) REVERT: D 845 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7498 (mm110) REVERT: G 110 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8485 (tt0) REVERT: G 233 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8432 (mmp80) REVERT: G 546 LYS cc_start: 0.8779 (mtmm) cc_final: 0.7793 (pmtt) REVERT: G 747 LYS cc_start: 0.8424 (mttt) cc_final: 0.7955 (mmmm) REVERT: G 758 PHE cc_start: 0.8277 (m-80) cc_final: 0.8029 (m-10) REVERT: G 845 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7626 (mm110) REVERT: I 110 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8487 (tt0) REVERT: I 233 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8437 (mmp80) REVERT: I 747 LYS cc_start: 0.8472 (mttt) cc_final: 0.8012 (mmmm) REVERT: I 758 PHE cc_start: 0.8396 (m-80) cc_final: 0.8156 (m-10) REVERT: I 845 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7588 (mm110) REVERT: J 110 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8572 (tt0) REVERT: J 479 MET cc_start: 0.8424 (ttm) cc_final: 0.8166 (ttm) REVERT: J 845 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7544 (mm110) REVERT: L 130 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8516 (mm110) REVERT: L 747 LYS cc_start: 0.8573 (mttt) cc_final: 0.8113 (mmmm) REVERT: L 845 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7494 (mm110) outliers start: 84 outliers final: 34 residues processed: 300 average time/residue: 1.0045 time to fit residues: 355.9553 Evaluate side-chains 259 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 823 LEU Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 823 LEU Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 9 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 411 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 349 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 468 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071483 restraints weight = 76871.645| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.93 r_work: 0.2783 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42708 Z= 0.118 Angle : 0.466 7.889 57666 Z= 0.233 Chirality : 0.040 0.145 6420 Planarity : 0.003 0.049 7374 Dihedral : 7.049 82.378 5796 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.63 % Allowed : 13.71 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.54 (0.12), residues: 5184 helix: 1.46 (0.11), residues: 2334 sheet: 0.22 (0.22), residues: 678 loop : 1.03 (0.15), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 580 TYR 0.010 0.001 TYR D 197 PHE 0.012 0.001 PHE D 782 TRP 0.015 0.001 TRP J 787 HIS 0.002 0.001 HIS G 486 Details of bonding type rmsd covalent geometry : bond 0.00281 (42708) covalent geometry : angle 0.46557 (57666) hydrogen bonds : bond 0.03046 ( 1859) hydrogen bonds : angle 4.29692 ( 5145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5475 (t-90) REVERT: B 110 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8556 (tt0) REVERT: B 479 MET cc_start: 0.8416 (ttm) cc_final: 0.8152 (ttm) REVERT: B 747 LYS cc_start: 0.8416 (mttt) cc_final: 0.7975 (mmmm) REVERT: B 845 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7541 (mm110) REVERT: D 100 HIS cc_start: 0.5921 (OUTLIER) cc_final: 0.5559 (t-90) REVERT: D 130 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (mm110) REVERT: D 747 LYS cc_start: 0.8514 (mttt) cc_final: 0.8030 (mmmm) REVERT: D 845 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7506 (mm110) REVERT: G 110 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8504 (tt0) REVERT: G 233 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8392 (mmp80) REVERT: G 546 LYS cc_start: 0.8765 (mtmm) cc_final: 0.7778 (pmtt) REVERT: G 747 LYS cc_start: 0.8409 (mttt) cc_final: 0.7943 (mmmm) REVERT: G 758 PHE cc_start: 0.8333 (m-80) cc_final: 0.8129 (m-10) REVERT: G 845 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7621 (mm110) REVERT: I 110 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8496 (tt0) REVERT: I 233 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8391 (mmp80) REVERT: I 546 LYS cc_start: 0.8772 (mtmm) cc_final: 0.7807 (pmtt) REVERT: I 747 LYS cc_start: 0.8451 (mttt) cc_final: 0.7989 (mmmm) REVERT: I 845 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7608 (mm110) REVERT: J 110 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8561 (tt0) REVERT: J 391 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8193 (mtmm) REVERT: J 845 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7559 (mm110) REVERT: L 100 HIS cc_start: 0.5932 (OUTLIER) cc_final: 0.5568 (t-90) REVERT: L 110 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8410 (tt0) REVERT: L 130 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8562 (mm110) REVERT: L 747 LYS cc_start: 0.8539 (mttt) cc_final: 0.8063 (mmmm) REVERT: L 845 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7507 (mm110) outliers start: 75 outliers final: 43 residues processed: 294 average time/residue: 0.9734 time to fit residues: 338.5668 Evaluate side-chains 272 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 796 ARG Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 823 LEU Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 396 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 633 THR Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 823 LEU Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 150 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 463 optimal weight: 2.9990 chunk 483 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.117667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070862 restraints weight = 76798.148| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.90 r_work: 0.2768 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42708 Z= 0.144 Angle : 0.480 8.046 57666 Z= 0.241 Chirality : 0.040 0.153 6420 Planarity : 0.004 0.052 7374 Dihedral : 7.043 81.835 5796 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.74 % Allowed : 13.82 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.52 (0.12), residues: 5184 helix: 1.45 (0.11), residues: 2334 sheet: 0.28 (0.22), residues: 672 loop : 0.99 (0.15), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 580 TYR 0.015 0.001 TYR D 127 PHE 0.013 0.001 PHE D 782 TRP 0.016 0.001 TRP J 787 HIS 0.002 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00345 (42708) covalent geometry : angle 0.47991 (57666) hydrogen bonds : bond 0.03187 ( 1859) hydrogen bonds : angle 4.31270 ( 5145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 234 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8589 (tt0) REVERT: B 391 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8263 (mtmm) REVERT: B 747 LYS cc_start: 0.8483 (mttt) cc_final: 0.8034 (mmmm) REVERT: B 763 MET cc_start: 0.9198 (tpp) cc_final: 0.8836 (mmm) REVERT: B 845 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7579 (mm110) REVERT: D 100 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.5595 (t-90) REVERT: D 110 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8410 (tt0) REVERT: D 130 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8591 (mm110) REVERT: D 747 LYS cc_start: 0.8550 (mttt) cc_final: 0.8078 (mmmm) REVERT: D 845 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7559 (mm110) REVERT: G 100 HIS cc_start: 0.5855 (OUTLIER) cc_final: 0.5537 (t-90) REVERT: G 110 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8503 (tt0) REVERT: G 233 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8405 (mmp80) REVERT: G 546 LYS cc_start: 0.8805 (mtmm) cc_final: 0.7854 (pmtt) REVERT: G 747 LYS cc_start: 0.8473 (mttt) cc_final: 0.8015 (mmmm) REVERT: G 845 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7634 (mm110) REVERT: I 100 HIS cc_start: 0.5882 (OUTLIER) cc_final: 0.5558 (t-90) REVERT: I 110 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8491 (tt0) REVERT: I 233 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8418 (mmp80) REVERT: I 546 LYS cc_start: 0.8814 (mtmm) cc_final: 0.7878 (pmtt) REVERT: I 747 LYS cc_start: 0.8514 (mttt) cc_final: 0.8045 (mmmm) REVERT: I 845 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7605 (mm110) REVERT: J 100 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5513 (t-90) REVERT: J 110 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8601 (tt0) REVERT: J 391 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8260 (mtmm) REVERT: J 763 MET cc_start: 0.9186 (tpp) cc_final: 0.8860 (mmm) REVERT: J 845 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (mm110) REVERT: L 100 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5622 (t-90) REVERT: L 110 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8407 (tt0) REVERT: L 747 LYS cc_start: 0.8568 (mttt) cc_final: 0.8094 (mmmm) REVERT: L 758 PHE cc_start: 0.8112 (m-80) cc_final: 0.7871 (m-80) REVERT: L 845 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7526 (mm110) outliers start: 80 outliers final: 45 residues processed: 300 average time/residue: 0.9488 time to fit residues: 339.7058 Evaluate side-chains 276 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 823 LEU Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 396 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 633 THR Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 823 LEU Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 484 optimal weight: 0.9990 chunk 395 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 397 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 494 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN J 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.070949 restraints weight = 77017.459| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.93 r_work: 0.2777 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42708 Z= 0.126 Angle : 0.482 8.254 57666 Z= 0.241 Chirality : 0.040 0.157 6420 Planarity : 0.004 0.054 7374 Dihedral : 7.001 82.052 5796 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.61 % Allowed : 14.21 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.53 (0.12), residues: 5184 helix: 1.45 (0.11), residues: 2334 sheet: 0.31 (0.22), residues: 666 loop : 1.00 (0.15), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 580 TYR 0.011 0.001 TYR D 197 PHE 0.013 0.001 PHE D 782 TRP 0.019 0.001 TRP J 787 HIS 0.002 0.001 HIS J 97 Details of bonding type rmsd covalent geometry : bond 0.00300 (42708) covalent geometry : angle 0.48174 (57666) hydrogen bonds : bond 0.03140 ( 1859) hydrogen bonds : angle 4.27312 ( 5145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8606 (tt0) REVERT: B 127 TYR cc_start: 0.8805 (m-80) cc_final: 0.8589 (m-80) REVERT: B 747 LYS cc_start: 0.8465 (mttt) cc_final: 0.8016 (mmmm) REVERT: B 763 MET cc_start: 0.9164 (tpp) cc_final: 0.8829 (mmm) REVERT: B 845 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7592 (mm110) REVERT: D 32 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: D 100 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5623 (t-90) REVERT: D 110 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8377 (tt0) REVERT: D 130 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8624 (mm110) REVERT: D 580 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8157 (ttp-110) REVERT: D 747 LYS cc_start: 0.8505 (mttt) cc_final: 0.8011 (mmmm) REVERT: D 845 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: G 73 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8431 (mp0) REVERT: G 100 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.5528 (t-90) REVERT: G 110 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8476 (tt0) REVERT: G 233 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8402 (mmp80) REVERT: G 546 LYS cc_start: 0.8811 (mtmm) cc_final: 0.7892 (pmtt) REVERT: G 747 LYS cc_start: 0.8468 (mttt) cc_final: 0.8007 (mmmm) REVERT: G 845 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7637 (mm110) REVERT: I 73 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8435 (mp0) REVERT: I 100 HIS cc_start: 0.5855 (OUTLIER) cc_final: 0.5537 (t-90) REVERT: I 110 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8462 (tt0) REVERT: I 233 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8403 (mmp80) REVERT: I 546 LYS cc_start: 0.8815 (mtmm) cc_final: 0.7887 (pmtt) REVERT: I 747 LYS cc_start: 0.8513 (mttt) cc_final: 0.8061 (mmmm) REVERT: I 845 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7614 (mm110) REVERT: J 110 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8567 (tt0) REVERT: J 479 MET cc_start: 0.8266 (ttm) cc_final: 0.7973 (ttt) REVERT: J 763 MET cc_start: 0.9204 (tpp) cc_final: 0.8877 (mmm) REVERT: J 845 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7596 (mm110) REVERT: L 32 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: L 100 HIS cc_start: 0.5922 (OUTLIER) cc_final: 0.5589 (t-90) REVERT: L 110 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8378 (tt0) REVERT: L 546 LYS cc_start: 0.8834 (mppt) cc_final: 0.7901 (pmtt) REVERT: L 738 LEU cc_start: 0.8440 (mm) cc_final: 0.8116 (mm) REVERT: L 747 LYS cc_start: 0.8558 (mttt) cc_final: 0.8086 (mmmm) REVERT: L 758 PHE cc_start: 0.8184 (m-80) cc_final: 0.7981 (m-80) REVERT: L 845 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7516 (mm110) outliers start: 74 outliers final: 45 residues processed: 294 average time/residue: 0.8933 time to fit residues: 314.5766 Evaluate side-chains 279 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 796 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 396 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 633 THR Chi-restraints excluded: chain J residue 845 GLN Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 823 LEU Chi-restraints excluded: chain L residue 845 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 283 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 chunk 504 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.115717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068737 restraints weight = 76956.165| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.90 r_work: 0.2732 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 42708 Z= 0.206 Angle : 0.527 8.309 57666 Z= 0.265 Chirality : 0.042 0.162 6420 Planarity : 0.004 0.060 7374 Dihedral : 7.227 82.934 5796 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.61 % Allowed : 14.49 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.39 (0.12), residues: 5184 helix: 1.34 (0.11), residues: 2334 sheet: 0.15 (0.22), residues: 672 loop : 0.95 (0.15), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 580 TYR 0.019 0.001 TYR L 127 PHE 0.014 0.001 PHE D 782 TRP 0.021 0.001 TRP J 787 HIS 0.003 0.001 HIS I 380 Details of bonding type rmsd covalent geometry : bond 0.00496 (42708) covalent geometry : angle 0.52679 (57666) hydrogen bonds : bond 0.03678 ( 1859) hydrogen bonds : angle 4.42118 ( 5145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 HIS cc_start: 0.5926 (OUTLIER) cc_final: 0.5580 (t-90) REVERT: B 110 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8583 (tt0) REVERT: B 391 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8304 (mtmm) REVERT: B 479 MET cc_start: 0.8436 (ttm) cc_final: 0.8219 (ttm) REVERT: B 747 LYS cc_start: 0.8535 (mttt) cc_final: 0.8087 (mmmm) REVERT: D 32 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: D 100 HIS cc_start: 0.5814 (OUTLIER) cc_final: 0.5526 (t-90) REVERT: D 110 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8384 (tt0) REVERT: D 130 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8622 (mm110) REVERT: D 747 LYS cc_start: 0.8619 (mttt) cc_final: 0.8133 (mmmm) REVERT: G 100 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5570 (t-90) REVERT: G 110 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8474 (tt0) REVERT: G 233 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8443 (mmp80) REVERT: G 510 GLN cc_start: 0.8568 (mm110) cc_final: 0.8061 (mp10) REVERT: G 546 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8011 (pptt) REVERT: G 747 LYS cc_start: 0.8498 (mttt) cc_final: 0.8060 (mmmm) REVERT: G 845 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7655 (mm110) REVERT: I 100 HIS cc_start: 0.5842 (OUTLIER) cc_final: 0.5528 (t-90) REVERT: I 110 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8449 (tt0) REVERT: I 233 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8457 (mmp80) REVERT: I 510 GLN cc_start: 0.8571 (mm110) cc_final: 0.8069 (mp10) REVERT: I 546 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8009 (pptt) REVERT: I 747 LYS cc_start: 0.8582 (mttt) cc_final: 0.8145 (mmmm) REVERT: I 845 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7639 (mm110) REVERT: J 100 HIS cc_start: 0.5912 (OUTLIER) cc_final: 0.5570 (t-90) REVERT: J 110 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8587 (tt0) REVERT: J 391 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8323 (mtmm) REVERT: L 32 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: L 100 HIS cc_start: 0.5792 (OUTLIER) cc_final: 0.5498 (t-90) REVERT: L 110 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8384 (tt0) REVERT: L 546 LYS cc_start: 0.8845 (mppt) cc_final: 0.7909 (pmtt) REVERT: L 580 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8145 (ttp-110) REVERT: L 738 LEU cc_start: 0.8554 (mm) cc_final: 0.8297 (mm) REVERT: L 747 LYS cc_start: 0.8609 (mttt) cc_final: 0.8125 (mmmm) outliers start: 74 outliers final: 43 residues processed: 292 average time/residue: 0.8119 time to fit residues: 281.4415 Evaluate side-chains 268 residues out of total 4602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain G residue 233 ARG Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain G residue 591 ILE Chi-restraints excluded: chain G residue 633 THR Chi-restraints excluded: chain G residue 763 MET Chi-restraints excluded: chain G residue 845 GLN Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 396 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 519 CYS Chi-restraints excluded: chain I residue 591 ILE Chi-restraints excluded: chain I residue 633 THR Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 823 LEU Chi-restraints excluded: chain I residue 845 GLN Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 519 CYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 633 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain L residue 519 CYS Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 591 ILE Chi-restraints excluded: chain L residue 796 ARG Chi-restraints excluded: chain L residue 823 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 449 optimal weight: 0.1980 chunk 204 optimal weight: 1.9990 chunk 296 optimal weight: 0.0980 chunk 378 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 306 optimal weight: 0.0060 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.118807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.072195 restraints weight = 76818.818| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.95 r_work: 0.2806 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42708 Z= 0.087 Angle : 0.482 8.220 57666 Z= 0.241 Chirality : 0.039 0.149 6420 Planarity : 0.004 0.052 7374 Dihedral : 7.018 81.930 5796 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.78 % Allowed : 15.38 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.47 (0.12), residues: 5184 helix: 1.43 (0.11), residues: 2334 sheet: -0.01 (0.21), residues: 726 loop : 1.06 (0.15), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 580 TYR 0.013 0.001 TYR J 127 PHE 0.014 0.001 PHE D 782 TRP 0.022 0.001 TRP B 787 HIS 0.003 0.001 HIS I 380 Details of bonding type rmsd covalent geometry : bond 0.00187 (42708) covalent geometry : angle 0.48186 (57666) hydrogen bonds : bond 0.02853 ( 1859) hydrogen bonds : angle 4.21242 ( 5145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13492.72 seconds wall clock time: 230 minutes 41.43 seconds (13841.43 seconds total)