Starting phenix.real_space_refine on Sat Oct 31 14:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.cif Found real_map, /net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33as_59308/10_2026/33as_59308.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 27252 2.51 5 N 7476 2.21 5 O 8232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43080 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3590 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 5.76, per 1000 atoms: 0.13 Number of scatterers: 43080 At special positions: 0 Unit cell: (179.49, 187.86, 175.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 8232 8.00 N 7476 7.00 C 27252 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: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10392 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 48 sheets defined 53.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP A 6 " --> pdb=" O ASP A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 11 through 26 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 118 through 134 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU A 165 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 213 through 229 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'B' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP B 6 " --> pdb=" O ASP B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 6' Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 118 through 134 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU B 165 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 213 through 229 Processing helix chain 'B' and resid 232 through 256 Processing helix chain 'B' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 420 removed outlier: 3.758A pdb=" N VAL B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP C 6 " --> pdb=" O ASP C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 118 through 134 Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU C 165 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 232 through 256 Processing helix chain 'C' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 420 removed outlier: 3.756A pdb=" N VAL C 415 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 457 through 463 Processing helix chain 'C' and resid 465 through 481 Processing helix chain 'D' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP D 6 " --> pdb=" O ASP D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 6' Processing helix chain 'D' and resid 11 through 26 Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.680A pdb=" N LEU D 165 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 232 through 256 Processing helix chain 'D' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 278 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 345 through 356 Processing helix chain 'D' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.525A pdb=" N MET D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'D' and resid 465 through 481 Processing helix chain 'E' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP E 6 " --> pdb=" O ASP E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 6' Processing helix chain 'E' and resid 11 through 26 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 118 through 134 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU E 165 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 213 through 229 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 297 through 308 Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.525A pdb=" N MET E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL E 415 " --> pdb=" O GLY E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 443 Processing helix chain 'E' and resid 457 through 463 Processing helix chain 'E' and resid 465 through 481 Processing helix chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP F 6 " --> pdb=" O ASP F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 11 through 26 Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 118 through 134 Processing helix chain 'F' and resid 162 through 166 removed outlier: 3.680A pdb=" N LEU F 165 " --> pdb=" O ARG F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 213 through 229 Processing helix chain 'F' and resid 232 through 256 Processing helix chain 'F' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY F 267 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 297 through 308 Processing helix chain 'F' and resid 321 through 333 Processing helix chain 'F' and resid 345 through 356 Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET F 396 " --> pdb=" O ALA F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL F 415 " --> pdb=" O GLY F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 443 Processing helix chain 'F' and resid 457 through 463 Processing helix chain 'F' and resid 465 through 481 Processing helix chain 'G' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP G 6 " --> pdb=" O ASP G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 11 through 26 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 43 through 56 Processing helix chain 'G' and resid 65 through 70 Processing helix chain 'G' and resid 118 through 134 Processing helix chain 'G' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU G 165 " --> pdb=" O ARG G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'G' and resid 213 through 229 Processing helix chain 'G' and resid 232 through 256 Processing helix chain 'G' and resid 260 through 285 removed outlier: 4.917A pdb=" N GLY G 267 " --> pdb=" O ALA G 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU G 268 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP G 278 " --> pdb=" O GLY G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 296 No H-bonds generated for 'chain 'G' and resid 294 through 296' Processing helix chain 'G' and resid 297 through 308 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'G' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET G 396 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 420 removed outlier: 3.758A pdb=" N VAL G 415 " --> pdb=" O GLY G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 Processing helix chain 'G' and resid 457 through 463 Processing helix chain 'G' and resid 465 through 481 Processing helix chain 'H' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP H 6 " --> pdb=" O ASP H 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 6' Processing helix chain 'H' and resid 11 through 26 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 43 through 56 Processing helix chain 'H' and resid 65 through 70 Processing helix chain 'H' and resid 118 through 134 Processing helix chain 'H' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU H 165 " --> pdb=" O ARG H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'H' and resid 213 through 229 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY H 267 " --> pdb=" O ALA H 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG H 270 " --> pdb=" O ARG H 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 278 " --> pdb=" O GLY H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 296 No H-bonds generated for 'chain 'H' and resid 294 through 296' Processing helix chain 'H' and resid 297 through 308 Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 345 through 356 Processing helix chain 'H' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET H 396 " --> pdb=" O ALA H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 420 removed outlier: 3.758A pdb=" N VAL H 415 " --> pdb=" O GLY H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 443 Processing helix chain 'H' and resid 457 through 463 Processing helix chain 'H' and resid 465 through 481 Processing helix chain 'I' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP I 6 " --> pdb=" O ASP I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 43 through 56 Processing helix chain 'I' and resid 65 through 70 Processing helix chain 'I' and resid 118 through 134 Processing helix chain 'I' and resid 162 through 166 removed outlier: 3.680A pdb=" N LEU I 165 " --> pdb=" O ARG I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 213 through 229 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 260 through 285 removed outlier: 4.917A pdb=" N GLY I 267 " --> pdb=" O ALA I 263 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 268 " --> pdb=" O LEU I 264 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 278 " --> pdb=" O GLY I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 296 No H-bonds generated for 'chain 'I' and resid 294 through 296' Processing helix chain 'I' and resid 297 through 308 Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 345 through 356 Processing helix chain 'I' and resid 366 through 376 removed outlier: 3.520A pdb=" N ILE I 376 " --> pdb=" O ALA I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 396 removed outlier: 3.525A pdb=" N MET I 396 " --> pdb=" O ALA I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 443 Processing helix chain 'I' and resid 457 through 463 Processing helix chain 'I' and resid 465 through 481 Processing helix chain 'J' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP J 6 " --> pdb=" O ASP J 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 3 through 6' Processing helix chain 'J' and resid 11 through 26 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 43 through 56 Processing helix chain 'J' and resid 65 through 70 Processing helix chain 'J' and resid 118 through 134 Processing helix chain 'J' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU J 165 " --> pdb=" O ARG J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix chain 'J' and resid 213 through 229 Processing helix chain 'J' and resid 232 through 256 Processing helix chain 'J' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY J 267 " --> pdb=" O ALA J 263 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU J 268 " --> pdb=" O LEU J 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG J 270 " --> pdb=" O ARG J 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 278 " --> pdb=" O GLY J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 296 No H-bonds generated for 'chain 'J' and resid 294 through 296' Processing helix chain 'J' and resid 297 through 308 Processing helix chain 'J' and resid 321 through 333 Processing helix chain 'J' and resid 345 through 356 Processing helix chain 'J' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE J 376 " --> pdb=" O ALA J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 396 removed outlier: 3.525A pdb=" N MET J 396 " --> pdb=" O ALA J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL J 415 " --> pdb=" O GLY J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 443 Processing helix chain 'J' and resid 457 through 463 Processing helix chain 'J' and resid 465 through 481 Processing helix chain 'K' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP K 6 " --> pdb=" O ASP K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3 through 6' Processing helix chain 'K' and resid 11 through 26 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 43 through 56 Processing helix chain 'K' and resid 65 through 70 Processing helix chain 'K' and resid 118 through 134 Processing helix chain 'K' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU K 165 " --> pdb=" O ARG K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 193 Processing helix chain 'K' and resid 207 through 209 No H-bonds generated for 'chain 'K' and resid 207 through 209' Processing helix chain 'K' and resid 213 through 229 Processing helix chain 'K' and resid 232 through 256 Processing helix chain 'K' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY K 267 " --> pdb=" O ALA K 263 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU K 268 " --> pdb=" O LEU K 264 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG K 270 " --> pdb=" O ARG K 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP K 278 " --> pdb=" O GLY K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 296 No H-bonds generated for 'chain 'K' and resid 294 through 296' Processing helix chain 'K' and resid 297 through 308 Processing helix chain 'K' and resid 321 through 333 Processing helix chain 'K' and resid 345 through 356 Processing helix chain 'K' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE K 376 " --> pdb=" O ALA K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 396 removed outlier: 3.525A pdb=" N MET K 396 " --> pdb=" O ALA K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 420 removed outlier: 3.758A pdb=" N VAL K 415 " --> pdb=" O GLY K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 443 Processing helix chain 'K' and resid 457 through 463 Processing helix chain 'K' and resid 465 through 481 Processing helix chain 'L' and resid 3 through 6 removed outlier: 3.693A pdb=" N ASP L 6 " --> pdb=" O ASP L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 3 through 6' Processing helix chain 'L' and resid 11 through 26 Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 43 through 56 Processing helix chain 'L' and resid 65 through 70 Processing helix chain 'L' and resid 118 through 134 Processing helix chain 'L' and resid 162 through 166 removed outlier: 3.681A pdb=" N LEU L 165 " --> pdb=" O ARG L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 193 Processing helix chain 'L' and resid 207 through 209 No H-bonds generated for 'chain 'L' and resid 207 through 209' Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 232 through 256 Processing helix chain 'L' and resid 260 through 285 removed outlier: 4.916A pdb=" N GLY L 267 " --> pdb=" O ALA L 263 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG L 270 " --> pdb=" O ARG L 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP L 278 " --> pdb=" O GLY L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 296 No H-bonds generated for 'chain 'L' and resid 294 through 296' Processing helix chain 'L' and resid 297 through 308 Processing helix chain 'L' and resid 321 through 333 Processing helix chain 'L' and resid 345 through 356 Processing helix chain 'L' and resid 366 through 376 removed outlier: 3.521A pdb=" N ILE L 376 " --> pdb=" O ALA L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 396 removed outlier: 3.524A pdb=" N MET L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 420 removed outlier: 3.757A pdb=" N VAL L 415 " --> pdb=" O GLY L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 443 Processing helix chain 'L' and resid 457 through 463 Processing helix chain 'L' and resid 465 through 481 Processing sheet with id=1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL A 96 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL A 30 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 112 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 29 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL A 139 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET A 31 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE A 141 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR A 33 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY A 143 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE A 35 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 198 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER A 138 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 200 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER A 140 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA A 202 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS A 142 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 204 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE A 144 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR A 80 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL A 360 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 338 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL A 361 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 340 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 312 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 287 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=5, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL B 96 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL B 30 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 112 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 29 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL B 139 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET B 31 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE B 141 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR B 33 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY B 143 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE B 35 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 198 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER B 138 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 200 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER B 140 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA B 202 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS B 142 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 204 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 144 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR B 80 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL B 360 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 338 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 361 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA B 340 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 312 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 287 " --> pdb=" O CYS B 450 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=9, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL C 96 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL C 30 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 112 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU C 29 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL C 139 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET C 31 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE C 141 " --> pdb=" O MET C 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR C 33 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY C 143 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE C 35 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 198 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER C 138 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 200 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 140 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA C 202 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS C 142 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 204 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE C 144 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR C 80 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL C 360 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 338 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL C 361 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA C 340 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA C 312 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 287 " --> pdb=" O CYS C 450 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=13, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL D 96 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL D 30 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY D 112 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU D 29 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL D 139 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET D 31 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE D 141 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR D 33 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY D 143 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE D 35 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU D 198 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER D 138 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL D 200 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER D 140 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA D 202 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS D 142 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL D 204 " --> pdb=" O HIS D 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 144 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR D 80 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL D 360 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 338 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 361 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA D 340 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA D 312 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 287 " --> pdb=" O CYS D 450 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 383 through 384 Processing sheet with id=17, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL E 96 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL E 30 " --> pdb=" O PRO E 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY E 112 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 29 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL E 139 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET E 31 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE E 141 " --> pdb=" O MET E 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR E 33 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY E 143 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE E 35 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU E 198 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER E 138 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL E 200 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER E 140 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA E 202 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS E 142 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 204 " --> pdb=" O HIS E 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE E 144 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR E 80 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 380 through 381 removed outlier: 6.972A pdb=" N VAL E 360 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 338 " --> pdb=" O PHE E 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL E 361 " --> pdb=" O ILE E 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA E 340 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA E 312 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 287 " --> pdb=" O CYS E 450 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 383 through 384 Processing sheet with id=21, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL F 96 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL F 30 " --> pdb=" O PRO F 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY F 112 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 29 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL F 139 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET F 31 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE F 141 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR F 33 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY F 143 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE F 35 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU F 198 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER F 138 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL F 200 " --> pdb=" O SER F 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER F 140 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA F 202 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS F 142 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL F 204 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE F 144 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR F 80 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL F 360 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE F 338 " --> pdb=" O PHE F 359 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL F 361 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA F 340 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA F 312 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 287 " --> pdb=" O CYS F 450 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 383 through 384 Processing sheet with id=25, first strand: chain 'G' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL G 96 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL G 30 " --> pdb=" O PRO G 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY G 112 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU G 29 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL G 139 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET G 31 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE G 141 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR G 33 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY G 143 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE G 35 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU G 198 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER G 138 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL G 200 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER G 140 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA G 202 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS G 142 " --> pdb=" O ALA G 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL G 204 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE G 144 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR G 80 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL G 360 " --> pdb=" O VAL G 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE G 338 " --> pdb=" O PHE G 359 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL G 361 " --> pdb=" O ILE G 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA G 340 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA G 312 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE G 287 " --> pdb=" O CYS G 450 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 383 through 384 Processing sheet with id=29, first strand: chain 'H' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL H 96 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL H 30 " --> pdb=" O PRO H 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY H 112 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU H 29 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL H 139 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET H 31 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE H 141 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR H 33 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLY H 143 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE H 35 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU H 198 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER H 138 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL H 200 " --> pdb=" O SER H 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER H 140 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA H 202 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS H 142 " --> pdb=" O ALA H 202 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL H 204 " --> pdb=" O HIS H 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE H 144 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR H 80 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'H' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL H 360 " --> pdb=" O VAL H 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE H 338 " --> pdb=" O PHE H 359 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL H 361 " --> pdb=" O ILE H 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA H 340 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA H 312 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 287 " --> pdb=" O CYS H 450 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 383 through 384 Processing sheet with id=33, first strand: chain 'I' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL I 96 " --> pdb=" O VAL I 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL I 30 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY I 112 " --> pdb=" O HIS I 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU I 29 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL I 139 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET I 31 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE I 141 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR I 33 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY I 143 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE I 35 " --> pdb=" O GLY I 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU I 198 " --> pdb=" O ARG I 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER I 138 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL I 200 " --> pdb=" O SER I 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER I 140 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA I 202 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS I 142 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL I 204 " --> pdb=" O HIS I 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE I 144 " --> pdb=" O VAL I 204 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 79 through 82 removed outlier: 6.545A pdb=" N THR I 80 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'I' and resid 380 through 381 removed outlier: 6.972A pdb=" N VAL I 360 " --> pdb=" O VAL I 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE I 338 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL I 361 " --> pdb=" O ILE I 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA I 340 " --> pdb=" O VAL I 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA I 312 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE I 287 " --> pdb=" O CYS I 450 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 383 through 384 Processing sheet with id=37, first strand: chain 'J' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL J 96 " --> pdb=" O VAL J 61 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL J 30 " --> pdb=" O PRO J 106 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY J 112 " --> pdb=" O HIS J 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU J 29 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL J 139 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET J 31 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE J 141 " --> pdb=" O MET J 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR J 33 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLY J 143 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE J 35 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU J 198 " --> pdb=" O ARG J 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER J 138 " --> pdb=" O LEU J 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL J 200 " --> pdb=" O SER J 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER J 140 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA J 202 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS J 142 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL J 204 " --> pdb=" O HIS J 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE J 144 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR J 80 " --> pdb=" O SER J 87 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL J 360 " --> pdb=" O VAL J 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE J 338 " --> pdb=" O PHE J 359 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL J 361 " --> pdb=" O ILE J 338 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA J 340 " --> pdb=" O VAL J 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA J 312 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 287 " --> pdb=" O CYS J 450 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'J' and resid 383 through 384 Processing sheet with id=41, first strand: chain 'K' and resid 8 through 10 removed outlier: 6.561A pdb=" N VAL K 96 " --> pdb=" O VAL K 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL K 30 " --> pdb=" O PRO K 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY K 112 " --> pdb=" O HIS K 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU K 29 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL K 139 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET K 31 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE K 141 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR K 33 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY K 143 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE K 35 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU K 198 " --> pdb=" O ARG K 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER K 138 " --> pdb=" O LEU K 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL K 200 " --> pdb=" O SER K 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER K 140 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA K 202 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS K 142 " --> pdb=" O ALA K 202 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL K 204 " --> pdb=" O HIS K 142 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE K 144 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR K 80 " --> pdb=" O SER K 87 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL K 360 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE K 338 " --> pdb=" O PHE K 359 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL K 361 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA K 340 " --> pdb=" O VAL K 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA K 312 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE K 287 " --> pdb=" O CYS K 450 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'K' and resid 383 through 384 Processing sheet with id=45, first strand: chain 'L' and resid 8 through 10 removed outlier: 6.562A pdb=" N VAL L 96 " --> pdb=" O VAL L 61 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL L 30 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY L 112 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU L 29 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL L 139 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET L 31 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE L 141 " --> pdb=" O MET L 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR L 33 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY L 143 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N PHE L 35 " --> pdb=" O GLY L 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU L 198 " --> pdb=" O ARG L 136 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER L 138 " --> pdb=" O LEU L 198 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL L 200 " --> pdb=" O SER L 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER L 140 " --> pdb=" O VAL L 200 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA L 202 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS L 142 " --> pdb=" O ALA L 202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL L 204 " --> pdb=" O HIS L 142 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE L 144 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.544A pdb=" N THR L 80 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'L' and resid 380 through 381 removed outlier: 6.973A pdb=" N VAL L 360 " --> pdb=" O VAL L 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE L 338 " --> pdb=" O PHE L 359 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL L 361 " --> pdb=" O ILE L 338 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA L 340 " --> pdb=" O VAL L 361 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA L 312 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 287 " --> pdb=" O CYS L 450 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'L' and resid 383 through 384 2316 hydrogen bonds defined for protein. 6840 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: 11.00 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14601 1.34 - 1.45: 4236 1.45 - 1.57: 24903 1.57 - 1.69: 0 1.69 - 1.80: 216 Bond restraints: 43956 Sorted by residual: bond pdb=" CA PRO K 214 " pdb=" C PRO K 214 " ideal model delta sigma weight residual 1.518 1.480 0.038 1.37e-02 5.33e+03 7.83e+00 bond pdb=" CA PRO J 214 " pdb=" C PRO J 214 " ideal model delta sigma weight residual 1.518 1.480 0.038 1.37e-02 5.33e+03 7.82e+00 bond pdb=" CA PRO C 214 " pdb=" C PRO C 214 " ideal model delta sigma weight residual 1.518 1.480 0.038 1.37e-02 5.33e+03 7.70e+00 bond pdb=" CA PRO A 214 " pdb=" C PRO A 214 " ideal model delta sigma weight residual 1.518 1.480 0.038 1.37e-02 5.33e+03 7.58e+00 bond pdb=" CA PRO H 214 " pdb=" C PRO H 214 " ideal model delta sigma weight residual 1.518 1.480 0.038 1.37e-02 5.33e+03 7.57e+00 ... (remaining 43951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 58650 1.74 - 3.48: 1122 3.48 - 5.22: 180 5.22 - 6.96: 36 6.96 - 8.70: 12 Bond angle restraints: 60000 Sorted by residual: angle pdb=" N PRO E 214 " pdb=" CA PRO E 214 " pdb=" C PRO E 214 " ideal model delta sigma weight residual 113.47 104.77 8.70 1.43e+00 4.89e-01 3.70e+01 angle pdb=" N PRO L 214 " pdb=" CA PRO L 214 " pdb=" C PRO L 214 " ideal model delta sigma weight residual 113.47 104.82 8.65 1.43e+00 4.89e-01 3.66e+01 angle pdb=" N PRO F 214 " pdb=" CA PRO F 214 " pdb=" C PRO F 214 " ideal model delta sigma weight residual 113.47 104.83 8.64 1.43e+00 4.89e-01 3.65e+01 angle pdb=" N PRO K 214 " pdb=" CA PRO K 214 " pdb=" C PRO K 214 " ideal model delta sigma weight residual 113.47 104.83 8.64 1.43e+00 4.89e-01 3.65e+01 angle pdb=" N PRO I 214 " pdb=" CA PRO I 214 " pdb=" C PRO I 214 " ideal model delta sigma weight residual 113.47 104.83 8.64 1.43e+00 4.89e-01 3.65e+01 ... (remaining 59995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 23231 18.04 - 36.09: 2257 36.09 - 54.13: 713 54.13 - 72.17: 187 72.17 - 90.22: 108 Dihedral angle restraints: 26496 sinusoidal: 10332 harmonic: 16164 Sorted by residual: dihedral pdb=" CB GLU H 249 " pdb=" CG GLU H 249 " pdb=" CD GLU H 249 " pdb=" OE1 GLU H 249 " ideal model delta sinusoidal sigma weight residual 0.00 -90.22 90.22 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU K 249 " pdb=" CG GLU K 249 " pdb=" CD GLU K 249 " pdb=" OE1 GLU K 249 " ideal model delta sinusoidal sigma weight residual 0.00 -90.20 90.20 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU F 249 " pdb=" CG GLU F 249 " pdb=" CD GLU F 249 " pdb=" OE1 GLU F 249 " ideal model delta sinusoidal sigma weight residual 0.00 -90.20 90.20 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 26493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4229 0.031 - 0.062: 1795 0.062 - 0.093: 529 0.093 - 0.124: 369 0.124 - 0.155: 50 Chirality restraints: 6972 Sorted by residual: chirality pdb=" CA ARG F 68 " pdb=" N ARG F 68 " pdb=" C ARG F 68 " pdb=" CB ARG F 68 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ARG G 68 " pdb=" N ARG G 68 " pdb=" C ARG G 68 " pdb=" CB ARG G 68 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ARG I 68 " pdb=" N ARG I 68 " pdb=" C ARG I 68 " pdb=" CB ARG I 68 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 6969 not shown) Planarity restraints: 7956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 212 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ALA L 212 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA L 212 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR L 213 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 212 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C ALA F 212 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA F 212 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR F 213 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 212 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C ALA G 212 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA G 212 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR G 213 " 0.010 2.00e-02 2.50e+03 ... (remaining 7953 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 16926 2.91 - 3.41: 43126 3.41 - 3.91: 73744 3.91 - 4.40: 84497 4.40 - 4.90: 144496 Nonbonded interactions: 362789 Sorted by model distance: nonbonded pdb=" O PRO E 214 " pdb=" N ALA E 217 " model vdw 2.414 3.120 nonbonded pdb=" O PRO K 214 " pdb=" N ALA K 217 " model vdw 2.415 3.120 nonbonded pdb=" O PRO B 214 " pdb=" N ALA B 217 " model vdw 2.415 3.120 nonbonded pdb=" O PRO C 214 " pdb=" N ALA C 217 " model vdw 2.415 3.120 nonbonded pdb=" O PRO A 214 " pdb=" N ALA A 217 " model vdw 2.415 3.120 ... (remaining 362784 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.700 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: 0.060 Extract box with map and model: 0.880 Check model and map are aligned: 0.220 Set scattering table: 0.100 Process input model: 36.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43956 Z= 0.196 Angle : 0.584 8.698 60000 Z= 0.337 Chirality : 0.043 0.155 6972 Planarity : 0.006 0.066 7956 Dihedral : 17.474 90.216 16104 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.19 % Allowed : 26.46 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.11), residues: 5628 helix: 0.04 (0.10), residues: 2712 sheet: -0.31 (0.18), residues: 1020 loop : -0.23 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 252 TYR 0.009 0.001 TYR B 33 PHE 0.006 0.001 PHE G 107 TRP 0.006 0.001 TRP L 454 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.20 (43956) covalent geometry : angle 0.58381 / 0.34 (60000) hydrogen bonds : bond 0.21626 / 14.70 ( 2316) hydrogen bonds : angle 7.83092 / 5.56 ( 6840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1241 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8224 (mtm) cc_final: 0.7963 (tmm) REVERT: A 329 LEU cc_start: 0.8111 (tp) cc_final: 0.7889 (tt) REVERT: A 414 MET cc_start: 0.8973 (tpp) cc_final: 0.8772 (tpt) REVERT: A 441 TYR cc_start: 0.8033 (m-80) cc_final: 0.7570 (m-80) REVERT: B 146 MET cc_start: 0.7309 (mmp) cc_final: 0.7108 (mmt) REVERT: B 152 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.7926 (tpp-160) REVERT: C 20 MET cc_start: 0.8243 (mtm) cc_final: 0.7933 (tmm) REVERT: C 110 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7843 (tt) REVERT: C 329 LEU cc_start: 0.8204 (tp) cc_final: 0.7843 (tt) REVERT: D 152 ARG cc_start: 0.8146 (mmt-90) cc_final: 0.7878 (tpp-160) REVERT: D 329 LEU cc_start: 0.8081 (tp) cc_final: 0.7768 (tt) REVERT: E 152 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7930 (tpp-160) REVERT: E 329 LEU cc_start: 0.8211 (tp) cc_final: 0.7864 (tt) REVERT: F 152 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7962 (tpp-160) REVERT: F 329 LEU cc_start: 0.8094 (tp) cc_final: 0.7758 (tt) REVERT: F 414 MET cc_start: 0.9005 (tpp) cc_final: 0.8785 (tpt) REVERT: F 441 TYR cc_start: 0.8040 (m-80) cc_final: 0.7785 (m-80) REVERT: G 110 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7961 (tt) REVERT: H 20 MET cc_start: 0.8276 (mtm) cc_final: 0.8011 (tmm) REVERT: H 329 LEU cc_start: 0.8111 (tp) cc_final: 0.7842 (tt) REVERT: H 441 TYR cc_start: 0.7979 (m-80) cc_final: 0.7375 (m-80) REVERT: I 110 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7975 (tt) REVERT: I 146 MET cc_start: 0.7629 (mmp) cc_final: 0.7286 (mmt) REVERT: I 152 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7871 (tpp-160) REVERT: I 329 LEU cc_start: 0.8211 (tp) cc_final: 0.7982 (tt) REVERT: J 20 MET cc_start: 0.8336 (mtm) cc_final: 0.8062 (tmm) REVERT: J 264 LEU cc_start: 0.9166 (tm) cc_final: 0.8942 (tm) REVERT: J 329 LEU cc_start: 0.8149 (tp) cc_final: 0.7866 (tt) REVERT: J 414 MET cc_start: 0.9010 (tpp) cc_final: 0.8802 (tpp) REVERT: K 146 MET cc_start: 0.7408 (mmp) cc_final: 0.7189 (mmt) REVERT: K 152 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7773 (tpp-160) REVERT: L 152 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7868 (tpp-160) REVERT: L 329 LEU cc_start: 0.8244 (tp) cc_final: 0.7958 (tt) REVERT: L 441 TYR cc_start: 0.8051 (m-80) cc_final: 0.7573 (m-80) outliers start: 99 outliers final: 5 residues processed: 1291 average time/residue: 0.2908 time to fit residues: 583.9037 Evaluate side-chains 616 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 608 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain L residue 278 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 0.6980 chunk 310 optimal weight: 0.0870 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 348 GLN A 446 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN B 280 GLN B 348 GLN B 446 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 280 GLN C 348 GLN C 446 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 348 GLN D 446 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 348 GLN E 446 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN F 348 GLN F 446 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN G 280 GLN G 348 GLN G 446 GLN H 100 GLN H 247 GLN H 348 GLN H 446 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN I 348 GLN I 446 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN J 348 GLN J 446 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 GLN K 280 GLN K 348 GLN K 446 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 GLN L 280 GLN L 348 GLN L 446 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112265 restraints weight = 89111.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115786 restraints weight = 49527.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.118044 restraints weight = 35147.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.119446 restraints weight = 28726.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120290 restraints weight = 25505.882| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43956 Z= 0.178 Angle : 0.644 11.461 60000 Z= 0.327 Chirality : 0.047 0.177 6972 Planarity : 0.005 0.045 7956 Dihedral : 4.360 44.943 6124 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.71 % Allowed : 20.91 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.11), residues: 5628 helix: 0.81 (0.10), residues: 2724 sheet: -0.42 (0.17), residues: 1020 loop : -0.28 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 245 TYR 0.028 0.002 TYR H 33 PHE 0.032 0.002 PHE A 107 TRP 0.035 0.002 TRP F 466 HIS 0.010 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (43956) covalent geometry : angle 0.64374 / 0.33 (60000) hydrogen bonds : bond 0.05142 / 3.49 ( 2316) hydrogen bonds : angle 5.08278 / 3.63 ( 6840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 749 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 LYS cc_start: 0.8679 (tptm) cc_final: 0.8469 (tptt) REVERT: B 20 MET cc_start: 0.8356 (tmm) cc_final: 0.8119 (tmm) REVERT: B 146 MET cc_start: 0.7248 (mmp) cc_final: 0.6995 (mmt) REVERT: B 152 ARG cc_start: 0.8350 (mmt-90) cc_final: 0.7983 (tpp-160) REVERT: B 224 ILE cc_start: 0.8368 (mm) cc_final: 0.8113 (mm) REVERT: B 235 ILE cc_start: 0.8029 (mt) cc_final: 0.7825 (tt) REVERT: B 244 HIS cc_start: 0.7961 (m90) cc_final: 0.7751 (m90) REVERT: B 329 LEU cc_start: 0.8868 (tp) cc_final: 0.8513 (tt) REVERT: C 116 ASP cc_start: 0.8145 (m-30) cc_final: 0.7905 (m-30) REVERT: C 276 ARG cc_start: 0.7355 (ptm160) cc_final: 0.7083 (ptm-80) REVERT: D 152 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.7942 (tpp-160) REVERT: E 152 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7958 (tpp-160) REVERT: F 152 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8013 (tpp-160) REVERT: F 329 LEU cc_start: 0.8593 (tp) cc_final: 0.8372 (tt) REVERT: G 276 ARG cc_start: 0.7461 (ptm160) cc_final: 0.7245 (ptm-80) REVERT: G 329 LEU cc_start: 0.8802 (tp) cc_final: 0.8499 (tt) REVERT: I 110 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7938 (tt) REVERT: I 146 MET cc_start: 0.7501 (mmp) cc_final: 0.7081 (mmt) REVERT: I 152 ARG cc_start: 0.8212 (mmt-90) cc_final: 0.7910 (tpp-160) REVERT: J 40 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: K 146 MET cc_start: 0.7444 (mmp) cc_final: 0.7181 (mmt) REVERT: K 152 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7817 (tpp-160) REVERT: K 329 LEU cc_start: 0.8864 (tp) cc_final: 0.8528 (tt) outliers start: 213 outliers final: 116 residues processed: 920 average time/residue: 0.2567 time to fit residues: 382.6812 Evaluate side-chains 619 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 501 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 280 GLN Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 280 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [117, 25, 62, 375, 507, 72, 527, 344, 229, 193, 353] chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 375 optimal weight: 4.9990 chunk 507 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 527 optimal weight: 0.9990 chunk 344 optimal weight: 0.0010 chunk 229 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN B 5 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN E 5 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 100 GLN G 5 GLN H 5 GLN I 5 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN L 5 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 GLN ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.142610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113939 restraints weight = 88614.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117468 restraints weight = 49012.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119709 restraints weight = 34671.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121079 restraints weight = 28304.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121917 restraints weight = 25086.884| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43956 Z= 0.140 Angle : 0.604 9.680 60000 Z= 0.303 Chirality : 0.046 0.166 6972 Planarity : 0.005 0.042 7956 Dihedral : 4.312 46.398 6120 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.38 % Allowed : 21.33 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.11), residues: 5628 helix: 1.03 (0.10), residues: 2700 sheet: -0.17 (0.17), residues: 996 loop : -0.16 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 471 TYR 0.028 0.002 TYR H 33 PHE 0.022 0.001 PHE A 107 TRP 0.043 0.002 TRP A 466 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (43956) covalent geometry : angle 0.60437 / 0.30 (60000) hydrogen bonds : bond 0.04493 / 3.05 ( 2316) hydrogen bonds : angle 4.63996 / 3.32 ( 6840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 606 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.8329 (tmm) cc_final: 0.8110 (tmm) REVERT: B 146 MET cc_start: 0.7363 (mmp) cc_final: 0.6994 (mmt) REVERT: B 152 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7978 (tpp-160) REVERT: B 244 HIS cc_start: 0.7937 (m90) cc_final: 0.7714 (m90) REVERT: B 329 LEU cc_start: 0.8828 (tp) cc_final: 0.8481 (tt) REVERT: D 152 ARG cc_start: 0.8224 (mmt-90) cc_final: 0.7800 (tpp-160) REVERT: D 264 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8995 (tm) REVERT: E 152 ARG cc_start: 0.8239 (mmt-90) cc_final: 0.7930 (tpp-160) REVERT: E 336 MET cc_start: 0.3795 (ttm) cc_final: 0.3585 (ttm) REVERT: F 152 ARG cc_start: 0.8297 (mmt-90) cc_final: 0.7997 (tpp-160) REVERT: G 276 ARG cc_start: 0.7432 (ptm160) cc_final: 0.6869 (ptm160) REVERT: G 329 LEU cc_start: 0.8735 (tp) cc_final: 0.8383 (tt) REVERT: H 264 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8913 (tm) REVERT: I 110 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7917 (tt) REVERT: I 146 MET cc_start: 0.7466 (mmp) cc_final: 0.7044 (mmt) REVERT: I 152 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.7915 (tpp-160) REVERT: J 40 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8693 (m-30) REVERT: K 152 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7814 (tpp-160) REVERT: K 329 LEU cc_start: 0.8797 (tp) cc_final: 0.8451 (tt) outliers start: 198 outliers final: 126 residues processed: 752 average time/residue: 0.2542 time to fit residues: 311.3712 Evaluate side-chains 630 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 500 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 426 ARG Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 418 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [159, 98, 117, 546, 23, 314, 93, 152, 65, 529, 195] chunk 159 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 546 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 529 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109892 restraints weight = 88675.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.113276 restraints weight = 50158.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115433 restraints weight = 35916.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116746 restraints weight = 29537.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117393 restraints weight = 26327.514| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 43956 Z= 0.193 Angle : 0.617 9.184 60000 Z= 0.312 Chirality : 0.047 0.164 6972 Planarity : 0.005 0.084 7956 Dihedral : 4.508 55.811 6120 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.73 % Allowed : 20.45 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.11), residues: 5628 helix: 0.99 (0.10), residues: 2724 sheet: -0.21 (0.17), residues: 996 loop : -0.15 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 471 TYR 0.030 0.002 TYR E 33 PHE 0.016 0.002 PHE A 107 TRP 0.054 0.003 TRP D 466 HIS 0.013 0.001 HIS F 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (43956) covalent geometry : angle 0.61742 / 0.31 (60000) hydrogen bonds : bond 0.04350 / 2.97 ( 2316) hydrogen bonds : angle 4.52100 / 3.23 ( 6840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 553 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.8361 (tmm) cc_final: 0.8109 (tmm) REVERT: B 146 MET cc_start: 0.7338 (mmp) cc_final: 0.6967 (mmt) REVERT: B 152 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.8024 (tpp-160) REVERT: B 329 LEU cc_start: 0.8883 (tp) cc_final: 0.8538 (tt) REVERT: C 116 ASP cc_start: 0.8226 (m-30) cc_final: 0.7901 (m-30) REVERT: D 264 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8981 (tm) REVERT: E 218 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8237 (mt) REVERT: E 455 MET cc_start: 0.7444 (mpp) cc_final: 0.7209 (mpp) REVERT: F 152 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8062 (tpp-160) REVERT: F 329 LEU cc_start: 0.8840 (tp) cc_final: 0.8487 (tt) REVERT: G 218 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8502 (tt) REVERT: G 329 LEU cc_start: 0.8712 (tp) cc_final: 0.8461 (tt) REVERT: H 264 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8999 (tm) REVERT: I 110 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7962 (tt) REVERT: I 146 MET cc_start: 0.7403 (mmp) cc_final: 0.7019 (mmt) REVERT: I 152 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7994 (tpp-160) REVERT: J 40 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8814 (m-30) REVERT: K 152 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.7870 (tpp-160) REVERT: K 218 LEU cc_start: 0.8667 (tt) cc_final: 0.8289 (mt) REVERT: K 329 LEU cc_start: 0.8792 (tp) cc_final: 0.8509 (tt) REVERT: L 368 ASN cc_start: 0.8318 (m-40) cc_final: 0.8096 (m110) outliers start: 214 outliers final: 166 residues processed: 713 average time/residue: 0.2500 time to fit residues: 294.6628 Evaluate side-chains 659 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 487 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 206 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 278 ASP Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [10, 118, 281, 428, 221, 345, 492, 175, 329, 426, 479] chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 428 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 492 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 426 optimal weight: 0.9980 chunk 479 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 HIS I 203 HIS ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN K 280 GLN ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.140135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111316 restraints weight = 88150.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.114694 restraints weight = 49682.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116856 restraints weight = 35503.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118186 restraints weight = 29169.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118988 restraints weight = 25967.666| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43956 Z= 0.152 Angle : 0.583 8.391 60000 Z= 0.296 Chirality : 0.046 0.165 6972 Planarity : 0.005 0.081 7956 Dihedral : 4.480 58.451 6120 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.53 % Allowed : 20.91 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.11), residues: 5628 helix: 0.99 (0.10), residues: 2724 sheet: -0.22 (0.16), residues: 996 loop : -0.21 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 252 TYR 0.032 0.002 TYR H 38 PHE 0.015 0.001 PHE A 107 TRP 0.028 0.002 TRP J 466 HIS 0.013 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (43956) covalent geometry : angle 0.58258 / 0.30 (60000) hydrogen bonds : bond 0.04126 / 2.82 ( 2316) hydrogen bonds : angle 4.37647 / 3.12 ( 6840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 541 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.8329 (tmm) cc_final: 0.8093 (tmm) REVERT: B 152 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.8001 (tpp-160) REVERT: B 329 LEU cc_start: 0.8807 (tp) cc_final: 0.8467 (tt) REVERT: D 218 LEU cc_start: 0.8556 (tt) cc_final: 0.8206 (mt) REVERT: D 264 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8996 (tm) REVERT: E 218 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8273 (mt) REVERT: E 455 MET cc_start: 0.7504 (mpp) cc_final: 0.7232 (mpp) REVERT: F 152 ARG cc_start: 0.8460 (mmt-90) cc_final: 0.8052 (tpp-160) REVERT: F 329 LEU cc_start: 0.8811 (tp) cc_final: 0.8428 (tt) REVERT: G 218 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8320 (mt) REVERT: G 329 LEU cc_start: 0.8711 (tp) cc_final: 0.8462 (tt) REVERT: H 264 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8987 (tm) REVERT: I 110 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7840 (tt) REVERT: I 146 MET cc_start: 0.7418 (mmp) cc_final: 0.6967 (mmt) REVERT: I 152 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.8002 (tpp-160) REVERT: J 40 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8801 (m-30) REVERT: K 152 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.7922 (tpp-160) REVERT: K 218 LEU cc_start: 0.8634 (tt) cc_final: 0.8296 (mt) REVERT: K 329 LEU cc_start: 0.8869 (tp) cc_final: 0.8564 (tt) outliers start: 205 outliers final: 165 residues processed: 692 average time/residue: 0.2503 time to fit residues: 285.9742 Evaluate side-chains 668 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 497 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 461 VAL Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 278 ASP Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 418 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [481, 453, 153, 142, 482, 459, 497, 72, 402, 441, 560] chunk 481 optimal weight: 3.9990 chunk 453 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 482 optimal weight: 0.7980 chunk 459 optimal weight: 0.9990 chunk 497 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 441 optimal weight: 2.9990 chunk 560 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN I 237 HIS ** I 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 HIS J 253 GLN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.141227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112660 restraints weight = 88493.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116035 restraints weight = 49761.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.118190 restraints weight = 35505.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119540 restraints weight = 29117.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120366 restraints weight = 25844.553| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43956 Z= 0.131 Angle : 0.570 10.629 60000 Z= 0.289 Chirality : 0.045 0.187 6972 Planarity : 0.005 0.083 7956 Dihedral : 4.417 58.594 6120 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.71 % Allowed : 21.33 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.11), residues: 5628 helix: 1.09 (0.10), residues: 2700 sheet: -0.16 (0.16), residues: 996 loop : -0.08 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 252 TYR 0.032 0.002 TYR D 38 PHE 0.014 0.001 PHE A 107 TRP 0.057 0.002 TRP D 466 HIS 0.015 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (43956) covalent geometry : angle 0.56978 / 0.29 (60000) hydrogen bonds : bond 0.03969 / 2.71 ( 2316) hydrogen bonds : angle 4.30715 / 3.08 ( 6840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 544 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 218 LEU cc_start: 0.8682 (tp) cc_final: 0.8365 (mt) REVERT: A 303 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7575 (mmtt) REVERT: B 20 MET cc_start: 0.8280 (tmm) cc_final: 0.8067 (tmm) REVERT: B 152 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.7984 (tpp-160) REVERT: B 314 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 329 LEU cc_start: 0.8780 (tp) cc_final: 0.8485 (tt) REVERT: D 218 LEU cc_start: 0.8451 (tt) cc_final: 0.8211 (mt) REVERT: D 264 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9008 (tm) REVERT: E 218 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8275 (mt) REVERT: E 336 MET cc_start: 0.4020 (ttm) cc_final: 0.3535 (ttt) REVERT: E 455 MET cc_start: 0.7479 (mpp) cc_final: 0.7179 (mpp) REVERT: F 218 LEU cc_start: 0.8627 (tp) cc_final: 0.8171 (mt) REVERT: F 314 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6500 (mm-30) REVERT: F 329 LEU cc_start: 0.8733 (tp) cc_final: 0.8340 (tt) REVERT: G 218 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8323 (mt) REVERT: G 329 LEU cc_start: 0.8643 (tp) cc_final: 0.8411 (tt) REVERT: H 264 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8999 (tm) REVERT: I 110 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7823 (tt) REVERT: I 146 MET cc_start: 0.7400 (mmp) cc_final: 0.6933 (mmt) REVERT: I 152 ARG cc_start: 0.8472 (mmt-90) cc_final: 0.7995 (tpp-160) REVERT: I 218 LEU cc_start: 0.8448 (tt) cc_final: 0.8246 (mt) REVERT: K 152 ARG cc_start: 0.8440 (mmt-90) cc_final: 0.7998 (tpp-160) REVERT: K 218 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8309 (mt) REVERT: K 224 ILE cc_start: 0.8460 (mm) cc_final: 0.8220 (mm) REVERT: K 329 LEU cc_start: 0.8783 (tp) cc_final: 0.8444 (tt) outliers start: 213 outliers final: 168 residues processed: 704 average time/residue: 0.2439 time to fit residues: 284.8248 Evaluate side-chains 669 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 494 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 278 ASP Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [173, 258, 464, 200, 289, 524, 1, 26, 476, 273, 119] chunk 173 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 464 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 289 optimal weight: 0.2980 chunk 524 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 476 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 HIS G 237 HIS G 253 GLN ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN L 237 HIS ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.141951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113639 restraints weight = 88217.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117029 restraints weight = 49561.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119225 restraints weight = 35286.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120559 restraints weight = 28813.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121371 restraints weight = 25588.750| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43956 Z= 0.122 Angle : 0.572 10.021 60000 Z= 0.291 Chirality : 0.045 0.196 6972 Planarity : 0.005 0.067 7956 Dihedral : 4.355 59.540 6120 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.33 % Allowed : 21.73 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.11), residues: 5628 helix: 1.17 (0.10), residues: 2688 sheet: -0.05 (0.16), residues: 984 loop : -0.05 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 252 TYR 0.031 0.002 TYR E 33 PHE 0.015 0.001 PHE A 107 TRP 0.056 0.002 TRP H 466 HIS 0.015 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (43956) covalent geometry : angle 0.57219 / 0.29 (60000) hydrogen bonds : bond 0.03877 / 2.65 ( 2316) hydrogen bonds : angle 4.24748 / 3.03 ( 6840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 515 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 218 LEU cc_start: 0.8674 (tp) cc_final: 0.8378 (mt) REVERT: A 314 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6500 (mm-30) REVERT: B 20 MET cc_start: 0.8240 (tmm) cc_final: 0.8023 (tmm) REVERT: B 152 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8216 (mmp80) REVERT: B 218 LEU cc_start: 0.8554 (tp) cc_final: 0.8314 (mt) REVERT: B 314 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 329 LEU cc_start: 0.8813 (tp) cc_final: 0.8597 (tt) REVERT: C 465 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: D 218 LEU cc_start: 0.8460 (tt) cc_final: 0.8255 (mt) REVERT: D 264 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9005 (tm) REVERT: E 218 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8248 (mt) REVERT: E 336 MET cc_start: 0.3895 (ttm) cc_final: 0.3631 (ttm) REVERT: E 455 MET cc_start: 0.7449 (mpp) cc_final: 0.7127 (mpp) REVERT: F 218 LEU cc_start: 0.8621 (tp) cc_final: 0.8230 (mt) REVERT: F 329 LEU cc_start: 0.8767 (tp) cc_final: 0.8369 (tt) REVERT: F 455 MET cc_start: 0.7263 (mpp) cc_final: 0.6976 (mpp) REVERT: G 218 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8245 (mt) REVERT: G 329 LEU cc_start: 0.8629 (tp) cc_final: 0.8372 (tt) REVERT: H 264 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8981 (tm) REVERT: I 110 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7793 (tt) REVERT: I 146 MET cc_start: 0.7416 (mmp) cc_final: 0.6931 (mmt) REVERT: I 152 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.7993 (tpp-160) REVERT: I 218 LEU cc_start: 0.8539 (tt) cc_final: 0.8316 (mt) REVERT: I 466 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.7266 (m-90) REVERT: K 152 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.8219 (mmp80) REVERT: K 218 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (mt) REVERT: K 329 LEU cc_start: 0.8807 (tp) cc_final: 0.8475 (tt) REVERT: L 218 LEU cc_start: 0.8557 (tp) cc_final: 0.8160 (mt) REVERT: L 303 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7500 (mmtt) REVERT: L 314 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6459 (mm-30) outliers start: 196 outliers final: 164 residues processed: 658 average time/residue: 0.2546 time to fit residues: 277.0496 Evaluate side-chains 664 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 491 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 466 TRP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 278 ASP Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [508, 547, 26, 12, 524, 185, 66, 95, 168, 252, 384] chunk 508 optimal weight: 0.7980 chunk 547 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 524 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN B 203 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 GLN ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 GLN K 280 GLN L 237 HIS ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113590 restraints weight = 88579.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116979 restraints weight = 49721.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119146 restraints weight = 35413.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120475 restraints weight = 28976.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121289 restraints weight = 25695.924| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 43956 Z= 0.127 Angle : 0.573 9.743 60000 Z= 0.292 Chirality : 0.045 0.195 6972 Planarity : 0.005 0.054 7956 Dihedral : 4.335 58.700 6120 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.55 % Allowed : 21.29 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.11), residues: 5628 helix: 1.17 (0.10), residues: 2700 sheet: -0.09 (0.16), residues: 984 loop : 0.01 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.029 0.002 TYR E 33 PHE 0.014 0.001 PHE A 107 TRP 0.052 0.002 TRP A 466 HIS 0.021 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (43956) covalent geometry : angle 0.57282 / 0.29 (60000) hydrogen bonds : bond 0.03815 / 2.60 ( 2316) hydrogen bonds : angle 4.24333 / 3.03 ( 6840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 511 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 218 LEU cc_start: 0.8666 (tp) cc_final: 0.8360 (mt) REVERT: B 20 MET cc_start: 0.8226 (tmm) cc_final: 0.8011 (tmm) REVERT: B 152 ARG cc_start: 0.8440 (mmt-90) cc_final: 0.8215 (mmp80) REVERT: B 213 TYR cc_start: 0.8296 (t80) cc_final: 0.8046 (t80) REVERT: B 218 LEU cc_start: 0.8532 (tp) cc_final: 0.8313 (mt) REVERT: B 314 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6547 (mm-30) REVERT: B 329 LEU cc_start: 0.8770 (tp) cc_final: 0.8555 (tt) REVERT: D 218 LEU cc_start: 0.8533 (tt) cc_final: 0.8269 (mt) REVERT: D 264 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8998 (tm) REVERT: E 218 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8277 (mt) REVERT: E 303 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7214 (mmtt) REVERT: E 336 MET cc_start: 0.3967 (ttm) cc_final: 0.3433 (ttt) REVERT: E 455 MET cc_start: 0.7429 (mpp) cc_final: 0.7136 (mpp) REVERT: E 459 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7671 (mmtm) REVERT: F 218 LEU cc_start: 0.8656 (tp) cc_final: 0.8253 (mt) REVERT: F 329 LEU cc_start: 0.8756 (tp) cc_final: 0.8354 (tt) REVERT: F 455 MET cc_start: 0.7264 (mpp) cc_final: 0.6982 (mpp) REVERT: G 218 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8251 (mt) REVERT: G 329 LEU cc_start: 0.8679 (tp) cc_final: 0.8425 (tt) REVERT: H 264 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8958 (tm) REVERT: H 303 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7510 (mmtt) REVERT: I 110 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7771 (tt) REVERT: I 146 MET cc_start: 0.7435 (mmp) cc_final: 0.6943 (mmt) REVERT: I 152 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.7990 (tpp-160) REVERT: I 218 LEU cc_start: 0.8479 (tt) cc_final: 0.8249 (mt) REVERT: I 224 ILE cc_start: 0.8598 (mm) cc_final: 0.8391 (mm) REVERT: I 253 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7280 (mm-40) REVERT: I 455 MET cc_start: 0.7284 (mpp) cc_final: 0.7032 (mpp) REVERT: K 152 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.8250 (mmp80) REVERT: K 218 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8227 (mt) REVERT: K 224 ILE cc_start: 0.8473 (mm) cc_final: 0.8216 (mm) REVERT: K 329 LEU cc_start: 0.8826 (tp) cc_final: 0.8501 (tt) REVERT: L 218 LEU cc_start: 0.8520 (tp) cc_final: 0.8150 (mt) REVERT: L 303 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7466 (mmtt) REVERT: L 314 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6502 (mm-30) outliers start: 206 outliers final: 173 residues processed: 660 average time/residue: 0.2488 time to fit residues: 272.5292 Evaluate side-chains 665 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 485 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 206 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 461 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 278 ASP Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 461 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [82, 352, 322, 280, 405, 225, 297, 158, 448, 518, 483] chunk 82 optimal weight: 0.7980 chunk 352 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 chunk 225 optimal weight: 0.1980 chunk 297 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 448 optimal weight: 9.9990 chunk 518 optimal weight: 0.9990 chunk 483 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.142557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114351 restraints weight = 88257.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117712 restraints weight = 49818.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119854 restraints weight = 35581.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121187 restraints weight = 29182.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121989 restraints weight = 25909.472| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43956 Z= 0.122 Angle : 0.568 9.510 60000 Z= 0.289 Chirality : 0.045 0.191 6972 Planarity : 0.004 0.047 7956 Dihedral : 4.278 55.920 6120 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.24 % Allowed : 21.97 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.11), residues: 5628 helix: 1.15 (0.10), residues: 2712 sheet: -0.13 (0.16), residues: 984 loop : 0.05 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 471 TYR 0.031 0.002 TYR E 33 PHE 0.014 0.001 PHE A 107 TRP 0.057 0.002 TRP J 466 HIS 0.021 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (43956) covalent geometry : angle 0.56757 / 0.29 (60000) hydrogen bonds : bond 0.03776 / 2.56 ( 2316) hydrogen bonds : angle 4.21584 / 3.01 ( 6840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 503 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (tt) REVERT: A 218 LEU cc_start: 0.8645 (tp) cc_final: 0.8355 (mt) REVERT: B 20 MET cc_start: 0.8207 (tmm) cc_final: 0.7996 (tmm) REVERT: B 152 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8206 (mmp80) REVERT: B 259 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: B 314 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6523 (mm-30) REVERT: B 329 LEU cc_start: 0.8774 (tp) cc_final: 0.8568 (tt) REVERT: D 218 LEU cc_start: 0.8505 (tt) cc_final: 0.8260 (mt) REVERT: D 264 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8976 (tm) REVERT: E 218 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8276 (mt) REVERT: E 303 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7236 (mmtt) REVERT: E 336 MET cc_start: 0.3899 (ttm) cc_final: 0.3688 (ttm) REVERT: F 213 TYR cc_start: 0.8233 (t80) cc_final: 0.8012 (t80) REVERT: F 218 LEU cc_start: 0.8626 (tp) cc_final: 0.8259 (mt) REVERT: F 455 MET cc_start: 0.7238 (mpp) cc_final: 0.6967 (mpp) REVERT: G 218 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8274 (mt) REVERT: G 329 LEU cc_start: 0.8724 (tp) cc_final: 0.8459 (tt) REVERT: H 264 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8947 (tm) REVERT: H 303 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7421 (mmtt) REVERT: I 110 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7775 (tt) REVERT: I 146 MET cc_start: 0.7436 (mmp) cc_final: 0.6946 (mmt) REVERT: I 218 LEU cc_start: 0.8492 (tt) cc_final: 0.8259 (mt) REVERT: I 253 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7207 (mm-40) REVERT: I 455 MET cc_start: 0.7282 (mpp) cc_final: 0.7039 (mpp) REVERT: J 218 LEU cc_start: 0.8639 (tp) cc_final: 0.8420 (mt) REVERT: K 152 ARG cc_start: 0.8486 (mmt-90) cc_final: 0.8223 (mmp80) REVERT: K 218 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (mt) REVERT: K 224 ILE cc_start: 0.8457 (mm) cc_final: 0.8170 (mm) REVERT: K 314 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6579 (mm-30) REVERT: K 329 LEU cc_start: 0.8815 (tp) cc_final: 0.8506 (tt) REVERT: L 218 LEU cc_start: 0.8499 (tp) cc_final: 0.8147 (mt) REVERT: L 314 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6374 (mm-30) outliers start: 192 outliers final: 166 residues processed: 646 average time/residue: 0.2467 time to fit residues: 265.2281 Evaluate side-chains 654 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 480 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 206 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 278 ASP Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 396 MET Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 461 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [209, 35, 126, 170, 291, 301, 128, 397, 325, 286, 387] chunk 209 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 chunk 301 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 397 optimal weight: 0.7980 chunk 325 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 387 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 HIS ** I 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 GLN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.142777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114558 restraints weight = 88727.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117937 restraints weight = 49912.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120099 restraints weight = 35533.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.121427 restraints weight = 29059.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122241 restraints weight = 25784.922| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43956 Z= 0.119 Angle : 0.571 9.413 60000 Z= 0.291 Chirality : 0.045 0.258 6972 Planarity : 0.005 0.066 7956 Dihedral : 4.150 53.756 6118 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.18 % Allowed : 22.13 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.11), residues: 5628 helix: 1.15 (0.10), residues: 2712 sheet: -0.14 (0.16), residues: 984 loop : 0.09 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 210 TYR 0.030 0.002 TYR E 33 PHE 0.014 0.001 PHE A 107 TRP 0.048 0.002 TRP J 466 HIS 0.024 0.001 HIS F 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (43956) covalent geometry : angle 0.57100 / 0.29 (60000) hydrogen bonds : bond 0.03737 / 2.53 ( 2316) hydrogen bonds : angle 4.20441 / 3.00 ( 6840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11256 Ramachandran restraints generated. 5628 Oldfield, 0 Emsley, 5628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 500 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 218 LEU cc_start: 0.8627 (tp) cc_final: 0.8348 (mt) REVERT: B 152 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.8190 (mmp80) REVERT: B 213 TYR cc_start: 0.8255 (t80) cc_final: 0.7984 (t80) REVERT: B 259 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: B 329 LEU cc_start: 0.8794 (tp) cc_final: 0.8594 (tt) REVERT: D 218 LEU cc_start: 0.8477 (tt) cc_final: 0.8254 (mt) REVERT: D 264 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8965 (tm) REVERT: E 218 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8277 (mt) REVERT: E 336 MET cc_start: 0.4060 (ttm) cc_final: 0.3781 (ttm) REVERT: E 455 MET cc_start: 0.7224 (mpp) cc_final: 0.6928 (mpp) REVERT: F 218 LEU cc_start: 0.8625 (tp) cc_final: 0.8259 (mt) REVERT: F 275 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7484 (mt-10) REVERT: F 455 MET cc_start: 0.7214 (mpp) cc_final: 0.6940 (mpp) REVERT: G 218 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8258 (mt) REVERT: G 329 LEU cc_start: 0.8741 (tp) cc_final: 0.8465 (tt) REVERT: H 264 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8923 (tm) REVERT: H 303 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7340 (mmtt) REVERT: H 455 MET cc_start: 0.7252 (mpp) cc_final: 0.6998 (mpp) REVERT: I 110 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7809 (tt) REVERT: I 146 MET cc_start: 0.7422 (mmp) cc_final: 0.6933 (mmt) REVERT: I 218 LEU cc_start: 0.8456 (tt) cc_final: 0.8227 (mt) REVERT: I 455 MET cc_start: 0.7259 (mpp) cc_final: 0.7021 (mpp) REVERT: K 152 ARG cc_start: 0.8475 (mmt-90) cc_final: 0.8214 (mmp80) REVERT: K 224 ILE cc_start: 0.8437 (mm) cc_final: 0.8146 (mm) REVERT: K 259 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: K 314 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6359 (mm-30) REVERT: K 329 LEU cc_start: 0.8810 (tp) cc_final: 0.8485 (tt) REVERT: L 218 LEU cc_start: 0.8499 (tp) cc_final: 0.8168 (mt) outliers start: 189 outliers final: 163 residues processed: 642 average time/residue: 0.2480 time to fit residues: 264.2177 Evaluate side-chains 650 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 479 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 206 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 399 THR Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 280 GLN Chi-restraints excluded: chain I residue 323 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 259 GLU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 186 VAL Chi-restraints excluded: chain L residue 192 GLN Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 399 THR Chi-restraints excluded: chain L residue 418 LEU Chi-restraints excluded: chain L residue 461 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: [351, 294, 257, 67, 210, 544, 31, 415, 14, 157, 527] chunk 351 optimal weight: 0.0050 chunk 294 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 544 optimal weight: 0.0770 chunk 31 optimal weight: 7.9990 chunk 415 optimal weight: 0.0470 chunk 14 optimal weight: 0.0270 chunk 157 optimal weight: 0.7980 chunk 527 optimal weight: 4.9990 overall best weight: 0.1708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN L 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.117138 restraints weight = 89226.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120558 restraints weight = 49674.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122734 restraints weight = 35068.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124100 restraints weight = 28537.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124747 restraints weight = 25228.859| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 43956 Z= 0.110 Angle : 0.571 9.761 60000 Z= 0.292 Chirality : 0.045 0.220 6972 Planarity : 0.005 0.056 7956 Dihedral : 3.874 51.798 6114 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.14 % Allowed : 23.32 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.11), residues: 5628 helix: 1.04 (0.10), residues: 2772 sheet: -0.07 (0.16), residues: 984 loop : 0.14 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 276 TYR 0.029 0.001 TYR E 33 PHE 0.014 0.001 PHE A 107 TRP 0.066 0.002 TRP H 466 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (43956) covalent geometry : angle 0.57086 / 0.29 (60000) hydrogen bonds : bond 0.03700 / 2.52 ( 2316) hydrogen bonds : angle 4.20830 / 3.01 ( 6840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8678.02 seconds wall clock time: 149 minutes 31.94 seconds (8971.94 seconds total)