Starting phenix.real_space_refine on Sun Feb 8 00:40:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5h_26350/02_2026/7u5h_26350.map" } resolution = 3.32 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 24 6.06 5 S 204 5.16 5 C 24816 2.51 5 N 6960 2.21 5 O 7188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39192 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3264 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.39, per 1000 atoms: 0.11 Number of scatterers: 39192 At special positions: 0 Unit cell: (157.29, 153.01, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 24 29.99 S 204 16.00 O 7188 8.00 N 6960 7.00 C 24816 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 436 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 90 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 436 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 90 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 436 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 90 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 436 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 90 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 436 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 90 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 436 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 90 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 436 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 90 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 436 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 90 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" NE2 HIS I 436 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 90 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" NE2 HIS J 436 " pdb=" ZN J 502 " pdb="ZN ZN J 502 " - pdb=" NE2 HIS J 90 " pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" NE2 HIS K 436 " pdb=" ZN K 502 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 90 " pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" NE2 HIS L 436 " pdb=" ZN L 502 " pdb="ZN ZN L 502 " - pdb=" NE2 HIS L 90 " 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9528 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 38.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 6 through 23 Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 327 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 284 removed outlier: 4.068A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 327 through 336 Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 444 through 466 removed outlier: 4.278A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Proline residue: B 462 - end of helix Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 327 through 336 Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 444 through 466 removed outlier: 4.278A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Proline residue: C 462 - end of helix Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 189 through 196 Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 327 through 336 Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'E' and resid 7 through 23 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 214 through 225 Processing helix chain 'E' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA E 278 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 327 through 336 Proline residue: E 334 - end of helix Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU E 448 " --> pdb=" O THR E 444 " (cutoff:3.500A) Proline residue: E 462 - end of helix Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 214 through 225 Processing helix chain 'F' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA F 278 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 327 through 336 Proline residue: F 334 - end of helix Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 413 through 422 Processing helix chain 'F' and resid 444 through 466 removed outlier: 4.280A pdb=" N LEU F 448 " --> pdb=" O THR F 444 " (cutoff:3.500A) Proline residue: F 462 - end of helix Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 189 through 196 Processing helix chain 'G' and resid 214 through 225 Processing helix chain 'G' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA G 278 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU G 282 " --> pdb=" O ALA G 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 310 through 321 Processing helix chain 'G' and resid 327 through 336 Proline residue: G 334 - end of helix Processing helix chain 'G' and resid 380 through 395 Processing helix chain 'G' and resid 413 through 422 Processing helix chain 'G' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU G 448 " --> pdb=" O THR G 444 " (cutoff:3.500A) Proline residue: G 462 - end of helix Processing helix chain 'H' and resid 7 through 23 Processing helix chain 'H' and resid 26 through 40 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 189 through 196 Processing helix chain 'H' and resid 214 through 225 Processing helix chain 'H' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA H 278 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU H 282 " --> pdb=" O ALA H 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 300 Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 327 through 336 Proline residue: H 334 - end of helix Processing helix chain 'H' and resid 380 through 395 Processing helix chain 'H' and resid 413 through 422 Processing helix chain 'H' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU H 448 " --> pdb=" O THR H 444 " (cutoff:3.500A) Proline residue: H 462 - end of helix Processing helix chain 'I' and resid 7 through 23 Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 189 through 196 Processing helix chain 'I' and resid 214 through 225 Processing helix chain 'I' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA I 278 " --> pdb=" O ASP I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 300 Processing helix chain 'I' and resid 310 through 321 Processing helix chain 'I' and resid 327 through 336 Proline residue: I 334 - end of helix Processing helix chain 'I' and resid 380 through 395 Processing helix chain 'I' and resid 413 through 422 Processing helix chain 'I' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU I 448 " --> pdb=" O THR I 444 " (cutoff:3.500A) Proline residue: I 462 - end of helix Processing helix chain 'J' and resid 7 through 23 Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 179 through 183 Processing helix chain 'J' and resid 189 through 196 Processing helix chain 'J' and resid 214 through 225 Processing helix chain 'J' and resid 261 through 278 removed outlier: 3.930A pdb=" N ALA J 278 " --> pdb=" O ASP J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 284 removed outlier: 4.068A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 300 Processing helix chain 'J' and resid 310 through 321 Processing helix chain 'J' and resid 327 through 336 Proline residue: J 334 - end of helix Processing helix chain 'J' and resid 380 through 395 Processing helix chain 'J' and resid 413 through 422 Processing helix chain 'J' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU J 448 " --> pdb=" O THR J 444 " (cutoff:3.500A) Proline residue: J 462 - end of helix Processing helix chain 'K' and resid 7 through 23 Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 189 through 196 Processing helix chain 'K' and resid 214 through 225 Processing helix chain 'K' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA K 278 " --> pdb=" O ASP K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 300 Processing helix chain 'K' and resid 310 through 321 Processing helix chain 'K' and resid 327 through 336 Proline residue: K 334 - end of helix Processing helix chain 'K' and resid 380 through 395 Processing helix chain 'K' and resid 413 through 422 Processing helix chain 'K' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU K 448 " --> pdb=" O THR K 444 " (cutoff:3.500A) Proline residue: K 462 - end of helix Processing helix chain 'L' and resid 7 through 23 Processing helix chain 'L' and resid 26 through 40 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 179 through 183 Processing helix chain 'L' and resid 189 through 196 Processing helix chain 'L' and resid 214 through 225 Processing helix chain 'L' and resid 261 through 278 removed outlier: 3.931A pdb=" N ALA L 278 " --> pdb=" O ASP L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 284 removed outlier: 4.067A pdb=" N LEU L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA L 284 " --> pdb=" O ALA L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 300 Processing helix chain 'L' and resid 310 through 321 Processing helix chain 'L' and resid 327 through 336 Proline residue: L 334 - end of helix Processing helix chain 'L' and resid 380 through 395 Processing helix chain 'L' and resid 413 through 422 Processing helix chain 'L' and resid 444 through 466 removed outlier: 4.279A pdb=" N LEU L 448 " --> pdb=" O THR L 444 " (cutoff:3.500A) Proline residue: L 462 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER A 58 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A 85 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 292 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 87 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 294 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 89 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 84 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 339 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 86 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA A 341 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 88 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A 338 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 428 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER A 340 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP A 427 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU A 96 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 236 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 231 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A 139 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR A 441 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS A 443 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 344 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER B 58 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER B 85 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA B 292 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 87 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR B 294 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 89 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 84 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE B 339 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 86 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA B 341 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY B 88 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET B 338 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 428 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER B 340 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP B 427 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU B 96 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 231 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 139 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 247 removed outlier: 3.539A pdb=" N THR B 441 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 443 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 344 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER C 58 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER C 85 " --> pdb=" O MET C 290 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 292 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 87 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR C 294 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 89 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 84 " --> pdb=" O TYR C 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 339 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU C 86 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA C 341 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY C 88 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET C 338 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 428 " --> pdb=" O MET C 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 340 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP C 427 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU C 96 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 231 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS C 139 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR C 441 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS C 443 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA C 344 " --> pdb=" O GLN C 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER D 58 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER D 85 " --> pdb=" O MET D 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA D 292 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 87 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR D 294 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 89 " --> pdb=" O TYR D 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE D 84 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 339 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 86 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA D 341 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 88 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET D 338 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU D 428 " --> pdb=" O MET D 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER D 340 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP D 427 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU D 96 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 236 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 231 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS D 139 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR D 441 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS D 443 " --> pdb=" O PRO D 431 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA D 344 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER E 58 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER E 85 " --> pdb=" O MET E 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA E 292 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 87 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR E 294 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA E 89 " --> pdb=" O TYR E 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE E 84 " --> pdb=" O TYR E 337 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE E 339 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU E 86 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA E 341 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY E 88 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET E 338 " --> pdb=" O LEU E 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU E 428 " --> pdb=" O MET E 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER E 340 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP E 427 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU E 96 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU E 236 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 231 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS E 139 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.541A pdb=" N THR E 441 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS E 443 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA E 344 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER F 58 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER F 85 " --> pdb=" O MET F 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA F 292 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 87 " --> pdb=" O ALA F 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR F 294 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA F 89 " --> pdb=" O TYR F 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE F 84 " --> pdb=" O TYR F 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE F 339 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU F 86 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA F 341 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY F 88 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET F 338 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU F 428 " --> pdb=" O MET F 338 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER F 340 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP F 427 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU F 96 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU F 236 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE F 231 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS F 139 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR F 441 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS F 443 " --> pdb=" O PRO F 431 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA F 344 " --> pdb=" O GLN F 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER G 58 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER G 85 " --> pdb=" O MET G 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA G 292 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE G 87 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR G 294 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA G 89 " --> pdb=" O TYR G 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE G 84 " --> pdb=" O TYR G 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE G 339 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU G 86 " --> pdb=" O ILE G 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA G 341 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY G 88 " --> pdb=" O ALA G 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET G 338 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU G 428 " --> pdb=" O MET G 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER G 340 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP G 427 " --> pdb=" O LYS G 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU G 96 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU G 236 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 231 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS G 139 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR G 441 " --> pdb=" O LEU G 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS G 443 " --> pdb=" O PRO G 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA G 344 " --> pdb=" O GLN G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER H 58 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER H 85 " --> pdb=" O MET H 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA H 292 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE H 87 " --> pdb=" O ALA H 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR H 294 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA H 89 " --> pdb=" O TYR H 294 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE H 84 " --> pdb=" O TYR H 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE H 339 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 86 " --> pdb=" O ILE H 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA H 341 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY H 88 " --> pdb=" O ALA H 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET H 338 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU H 428 " --> pdb=" O MET H 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER H 340 " --> pdb=" O LEU H 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP H 427 " --> pdb=" O LYS H 370 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 114 through 117 removed outlier: 4.479A pdb=" N LEU H 96 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU H 236 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE H 231 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS H 139 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR H 441 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS H 443 " --> pdb=" O PRO H 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA H 344 " --> pdb=" O GLN H 432 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER I 58 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER I 85 " --> pdb=" O MET I 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA I 292 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE I 87 " --> pdb=" O ALA I 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR I 294 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA I 89 " --> pdb=" O TYR I 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE I 84 " --> pdb=" O TYR I 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE I 339 " --> pdb=" O PHE I 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU I 86 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA I 341 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY I 88 " --> pdb=" O ALA I 341 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 338 " --> pdb=" O LEU I 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU I 428 " --> pdb=" O MET I 338 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER I 340 " --> pdb=" O LEU I 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP I 427 " --> pdb=" O LYS I 370 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 114 through 117 removed outlier: 4.481A pdb=" N LEU I 96 " --> pdb=" O LEU I 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU I 236 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE I 231 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS I 139 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR I 441 " --> pdb=" O LEU I 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS I 443 " --> pdb=" O PRO I 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA I 344 " --> pdb=" O GLN I 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.638A pdb=" N SER J 58 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER J 85 " --> pdb=" O MET J 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA J 292 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE J 87 " --> pdb=" O ALA J 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR J 294 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA J 89 " --> pdb=" O TYR J 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE J 84 " --> pdb=" O TYR J 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE J 339 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU J 86 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA J 341 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY J 88 " --> pdb=" O ALA J 341 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET J 338 " --> pdb=" O LEU J 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU J 428 " --> pdb=" O MET J 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER J 340 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP J 427 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU J 96 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU J 236 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE J 231 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS J 139 " --> pdb=" O ILE J 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR J 441 " --> pdb=" O LEU J 433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS J 443 " --> pdb=" O PRO J 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA J 344 " --> pdb=" O GLN J 432 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER K 58 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER K 85 " --> pdb=" O MET K 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA K 292 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE K 87 " --> pdb=" O ALA K 292 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR K 294 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA K 89 " --> pdb=" O TYR K 294 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE K 84 " --> pdb=" O TYR K 337 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE K 339 " --> pdb=" O PHE K 84 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU K 86 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA K 341 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY K 88 " --> pdb=" O ALA K 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET K 338 " --> pdb=" O LEU K 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU K 428 " --> pdb=" O MET K 338 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER K 340 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP K 427 " --> pdb=" O LYS K 370 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU K 96 " --> pdb=" O LEU K 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU K 236 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE K 231 " --> pdb=" O LYS K 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS K 139 " --> pdb=" O ILE K 231 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 245 through 247 removed outlier: 3.541A pdb=" N THR K 441 " --> pdb=" O LEU K 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS K 443 " --> pdb=" O PRO K 431 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA K 344 " --> pdb=" O GLN K 432 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 45 removed outlier: 3.639A pdb=" N SER L 58 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER L 85 " --> pdb=" O MET L 290 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA L 292 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE L 87 " --> pdb=" O ALA L 292 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR L 294 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA L 89 " --> pdb=" O TYR L 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE L 84 " --> pdb=" O TYR L 337 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE L 339 " --> pdb=" O PHE L 84 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU L 86 " --> pdb=" O ILE L 339 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA L 341 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY L 88 " --> pdb=" O ALA L 341 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET L 338 " --> pdb=" O LEU L 426 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU L 428 " --> pdb=" O MET L 338 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER L 340 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP L 427 " --> pdb=" O LYS L 370 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 114 through 117 removed outlier: 4.480A pdb=" N LEU L 96 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU L 236 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE L 231 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS L 139 " --> pdb=" O ILE L 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 245 through 247 removed outlier: 3.540A pdb=" N THR L 441 " --> pdb=" O LEU L 433 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS L 443 " --> pdb=" O PRO L 431 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA L 344 " --> pdb=" O GLN L 432 " (cutoff:3.500A) 1801 hydrogen bonds defined for protein. 4899 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: 9.87 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10587 1.33 - 1.45: 6610 1.45 - 1.57: 22451 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 39948 Sorted by residual: bond pdb=" CA THR L 189 " pdb=" C THR L 189 " ideal model delta sigma weight residual 1.522 1.471 0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" CA THR K 189 " pdb=" C THR K 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR E 189 " pdb=" C THR E 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR B 189 " pdb=" C THR B 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" CA THR J 189 " pdb=" C THR J 189 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.20e-02 6.94e+03 1.82e+01 ... (remaining 39943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 51078 1.70 - 3.41: 2212 3.41 - 5.11: 593 5.11 - 6.82: 177 6.82 - 8.52: 72 Bond angle restraints: 54132 Sorted by residual: angle pdb=" N LEU J 262 " pdb=" CA LEU J 262 " pdb=" C LEU J 262 " ideal model delta sigma weight residual 113.18 104.73 8.45 1.21e+00 6.83e-01 4.87e+01 angle pdb=" N LEU A 262 " pdb=" CA LEU A 262 " pdb=" C LEU A 262 " ideal model delta sigma weight residual 113.18 104.75 8.43 1.21e+00 6.83e-01 4.85e+01 angle pdb=" N LEU G 262 " pdb=" CA LEU G 262 " pdb=" C LEU G 262 " ideal model delta sigma weight residual 113.18 104.77 8.41 1.21e+00 6.83e-01 4.83e+01 angle pdb=" N LEU F 262 " pdb=" CA LEU F 262 " pdb=" C LEU F 262 " ideal model delta sigma weight residual 113.18 104.77 8.41 1.21e+00 6.83e-01 4.83e+01 angle pdb=" N LEU K 262 " pdb=" CA LEU K 262 " pdb=" C LEU K 262 " ideal model delta sigma weight residual 113.18 104.78 8.40 1.21e+00 6.83e-01 4.82e+01 ... (remaining 54127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 21603 14.52 - 29.04: 1749 29.04 - 43.56: 576 43.56 - 58.07: 252 58.07 - 72.59: 84 Dihedral angle restraints: 24264 sinusoidal: 9636 harmonic: 14628 Sorted by residual: dihedral pdb=" N ASN B 261 " pdb=" C ASN B 261 " pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " ideal model delta harmonic sigma weight residual 122.80 136.34 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N ASN D 261 " pdb=" C ASN D 261 " pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " ideal model delta harmonic sigma weight residual 122.80 136.33 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N ASN L 261 " pdb=" C ASN L 261 " pdb=" CA ASN L 261 " pdb=" CB ASN L 261 " ideal model delta harmonic sigma weight residual 122.80 136.32 -13.52 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 24261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6036 0.131 - 0.263: 162 0.263 - 0.394: 42 0.394 - 0.525: 12 0.525 - 0.656: 12 Chirality restraints: 6264 Sorted by residual: chirality pdb=" CA ASN G 261 " pdb=" N ASN G 261 " pdb=" C ASN G 261 " pdb=" CB ASN G 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASN B 261 " pdb=" N ASN B 261 " pdb=" C ASN B 261 " pdb=" CB ASN B 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASN D 261 " pdb=" N ASN D 261 " pdb=" C ASN D 261 " pdb=" CB ASN D 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 6261 not shown) Planarity restraints: 6972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY G 414 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO G 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO G 415 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 415 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 414 " 0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO E 415 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 415 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 415 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 414 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 415 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.033 5.00e-02 4.00e+02 ... (remaining 6969 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 60 2.12 - 2.81: 11332 2.81 - 3.51: 54905 3.51 - 4.20: 99182 4.20 - 4.90: 175991 Nonbonded interactions: 341470 Sorted by model distance: nonbonded pdb=" OD1 ASP A 342 " pdb="ZN ZN A 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP J 342 " pdb="ZN ZN J 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP D 342 " pdb="ZN ZN D 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP B 342 " pdb="ZN ZN B 502 " model vdw 1.424 2.230 nonbonded pdb=" OD1 ASP I 342 " pdb="ZN ZN I 502 " model vdw 1.424 2.230 ... (remaining 341465 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: 0.15 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 38.570 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.009 0.256 39972 Z= 0.440 Angle : 0.945 8.525 54132 Z= 0.583 Chirality : 0.068 0.656 6264 Planarity : 0.006 0.057 6972 Dihedral : 14.002 72.593 14736 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.32 % Allowed : 7.56 % Favored : 87.11 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.11), residues: 4944 helix: 0.67 (0.13), residues: 1632 sheet: -0.21 (0.15), residues: 1104 loop : -1.12 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 318 TYR 0.011 0.001 TYR C 337 PHE 0.018 0.002 PHE D 461 TRP 0.007 0.002 TRP C 122 HIS 0.009 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00636 (39948) covalent geometry : angle 0.94480 (54132) hydrogen bonds : bond 0.13816 ( 1801) hydrogen bonds : angle 5.96279 ( 4899) metal coordination : bond 0.24649 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 1223 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7428 (tptt) REVERT: A 111 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 115 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6483 (tm-30) REVERT: A 147 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5806 (pm20) REVERT: A 193 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: A 194 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 227 SER cc_start: 0.8206 (m) cc_final: 0.7665 (t) REVERT: A 251 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7305 (mp0) REVERT: A 261 ASN cc_start: 0.6418 (m-40) cc_final: 0.6168 (m-40) REVERT: A 270 GLN cc_start: 0.8009 (tp40) cc_final: 0.7177 (tp40) REVERT: A 274 ASP cc_start: 0.8735 (m-30) cc_final: 0.8283 (m-30) REVERT: A 297 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 326 LEU cc_start: 0.8688 (mp) cc_final: 0.8457 (mt) REVERT: A 372 ASN cc_start: 0.6321 (t0) cc_final: 0.5954 (t0) REVERT: B 19 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7964 (mtmm) REVERT: B 99 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6809 (tptp) REVERT: B 115 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6510 (tm-30) REVERT: B 147 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5432 (pm20) REVERT: B 227 SER cc_start: 0.7902 (m) cc_final: 0.7423 (t) REVERT: B 235 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 251 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7037 (mp0) REVERT: B 261 ASN cc_start: 0.6574 (m-40) cc_final: 0.5530 (m-40) REVERT: B 273 ILE cc_start: 0.8309 (mt) cc_final: 0.8087 (pt) REVERT: B 297 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 318 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7887 (mtp180) REVERT: B 326 LEU cc_start: 0.8303 (mp) cc_final: 0.7969 (mt) REVERT: B 331 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 365 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7519 (mtpp) REVERT: B 371 VAL cc_start: 0.8310 (t) cc_final: 0.8009 (m) REVERT: B 372 ASN cc_start: 0.6200 (t0) cc_final: 0.5833 (t0) REVERT: B 423 LEU cc_start: 0.9073 (tp) cc_final: 0.8728 (tt) REVERT: B 460 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8161 (tp) REVERT: C 19 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8172 (mtmt) REVERT: C 34 CYS cc_start: 0.8268 (m) cc_final: 0.8026 (m) REVERT: C 97 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7660 (mmt-90) REVERT: C 99 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7240 (tptp) REVERT: C 111 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: C 147 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5870 (pm20) REVERT: C 193 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: C 194 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: C 227 SER cc_start: 0.8232 (m) cc_final: 0.7760 (t) REVERT: C 251 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7223 (mp0) REVERT: C 261 ASN cc_start: 0.6774 (m-40) cc_final: 0.6555 (m-40) REVERT: C 290 MET cc_start: 0.8837 (ttp) cc_final: 0.8620 (ttp) REVERT: C 297 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 326 LEU cc_start: 0.7855 (mp) cc_final: 0.7557 (mp) REVERT: C 423 LEU cc_start: 0.9079 (tp) cc_final: 0.8867 (tt) REVERT: D 60 TYR cc_start: 0.7941 (m-80) cc_final: 0.7578 (m-80) REVERT: D 97 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7405 (mmm160) REVERT: D 147 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5691 (pm20) REVERT: D 179 MET cc_start: 0.7358 (tpt) cc_final: 0.6987 (tpt) REVERT: D 251 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7228 (mp0) REVERT: D 270 GLN cc_start: 0.8376 (tp40) cc_final: 0.8010 (tp40) REVERT: D 274 ASP cc_start: 0.8550 (m-30) cc_final: 0.8348 (m-30) REVERT: D 282 LEU cc_start: 0.8639 (tp) cc_final: 0.8392 (tp) REVERT: D 290 MET cc_start: 0.8788 (ttp) cc_final: 0.8379 (ttp) REVERT: D 296 ASN cc_start: 0.8864 (m-40) cc_final: 0.8656 (m-40) REVERT: D 326 LEU cc_start: 0.7984 (mp) cc_final: 0.7712 (mt) REVERT: D 372 ASN cc_start: 0.5891 (t0) cc_final: 0.5688 (t0) REVERT: D 435 MET cc_start: 0.6344 (ttp) cc_final: 0.5900 (ttp) REVERT: D 460 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8103 (tp) REVERT: E 19 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7924 (mtmt) REVERT: E 46 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7177 (mm) REVERT: E 97 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7783 (mmt180) REVERT: E 99 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7389 (tmtt) REVERT: E 132 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8783 (mt) REVERT: E 147 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: E 192 GLN cc_start: 0.8039 (mm110) cc_final: 0.7768 (mm-40) REVERT: E 193 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: E 194 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: E 251 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7300 (mm-30) REVERT: E 297 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7804 (tm-30) REVERT: E 326 LEU cc_start: 0.7747 (mp) cc_final: 0.7468 (mp) REVERT: E 435 MET cc_start: 0.6185 (ttp) cc_final: 0.5596 (ttp) REVERT: F 97 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7800 (mmt180) REVERT: F 147 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5765 (pm20) REVERT: F 179 MET cc_start: 0.7483 (tpt) cc_final: 0.7032 (mmm) REVERT: F 193 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: F 194 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: F 227 SER cc_start: 0.8191 (m) cc_final: 0.7728 (t) REVERT: F 251 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7255 (mp0) REVERT: F 261 ASN cc_start: 0.6443 (m-40) cc_final: 0.5272 (m-40) REVERT: F 265 CYS cc_start: 0.8526 (m) cc_final: 0.8056 (m) REVERT: F 274 ASP cc_start: 0.8684 (m-30) cc_final: 0.8410 (m-30) REVERT: F 297 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7752 (tm-30) REVERT: F 331 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6808 (mt-10) REVERT: F 371 VAL cc_start: 0.8517 (t) cc_final: 0.8261 (m) REVERT: F 372 ASN cc_start: 0.5947 (t0) cc_final: 0.5639 (t0) REVERT: F 460 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8089 (tp) REVERT: G 60 TYR cc_start: 0.8085 (m-80) cc_final: 0.7706 (m-80) REVERT: G 92 ASP cc_start: 0.8367 (p0) cc_final: 0.8090 (p0) REVERT: G 97 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7480 (mmt180) REVERT: G 99 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7390 (tptt) REVERT: G 115 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6602 (tm-30) REVERT: G 147 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5740 (pm20) REVERT: G 193 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: G 194 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: G 237 CYS cc_start: 0.8108 (m) cc_final: 0.7636 (m) REVERT: G 251 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7291 (mp0) REVERT: G 261 ASN cc_start: 0.6711 (m-40) cc_final: 0.6413 (m-40) REVERT: G 270 GLN cc_start: 0.8258 (tp40) cc_final: 0.7556 (tp40) REVERT: G 274 ASP cc_start: 0.8604 (m-30) cc_final: 0.8206 (m-30) REVERT: G 290 MET cc_start: 0.8883 (ttp) cc_final: 0.8613 (ttp) REVERT: G 326 LEU cc_start: 0.7825 (mp) cc_final: 0.7495 (mp) REVERT: G 371 VAL cc_start: 0.8546 (t) cc_final: 0.8284 (m) REVERT: G 372 ASN cc_start: 0.5898 (t0) cc_final: 0.5658 (t0) REVERT: G 389 GLU cc_start: 0.7703 (tp30) cc_final: 0.7240 (tp30) REVERT: G 460 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8146 (tt) REVERT: H 34 CYS cc_start: 0.7999 (m) cc_final: 0.7786 (m) REVERT: H 99 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6889 (tptp) REVERT: H 147 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5949 (pm20) REVERT: H 194 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: H 226 LEU cc_start: 0.7734 (mt) cc_final: 0.7519 (mt) REVERT: H 227 SER cc_start: 0.8239 (m) cc_final: 0.7608 (t) REVERT: H 251 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7191 (mp0) REVERT: H 261 ASN cc_start: 0.6152 (m-40) cc_final: 0.5522 (m-40) REVERT: H 270 GLN cc_start: 0.8218 (tp40) cc_final: 0.7771 (tp40) REVERT: H 297 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7599 (tm-30) REVERT: H 326 LEU cc_start: 0.8534 (mp) cc_final: 0.8243 (mt) REVERT: H 331 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6887 (mt-10) REVERT: H 345 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6756 (p-80) REVERT: H 365 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7715 (mtpp) REVERT: H 372 ASN cc_start: 0.5944 (t0) cc_final: 0.5665 (t0) REVERT: I 46 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (mm) REVERT: I 97 ARG cc_start: 0.8002 (mmt180) cc_final: 0.7499 (mmt-90) REVERT: I 99 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7082 (tptp) REVERT: I 115 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6597 (tm-30) REVERT: I 139 LYS cc_start: 0.6159 (tmtt) cc_final: 0.5954 (tptp) REVERT: I 147 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5319 (pm20) REVERT: I 227 SER cc_start: 0.8186 (m) cc_final: 0.7627 (t) REVERT: I 251 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7248 (mp0) REVERT: I 261 ASN cc_start: 0.6176 (m-40) cc_final: 0.5823 (m-40) REVERT: I 297 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 326 LEU cc_start: 0.8206 (mp) cc_final: 0.7997 (mt) REVERT: I 360 ARG cc_start: 0.5052 (mtp180) cc_final: 0.3513 (ptp-170) REVERT: I 365 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7716 (mtpp) REVERT: I 459 GLU cc_start: 0.7545 (pp20) cc_final: 0.7286 (pp20) REVERT: I 460 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8115 (tp) REVERT: J 34 CYS cc_start: 0.8288 (m) cc_final: 0.7963 (m) REVERT: J 46 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7428 (mm) REVERT: J 60 TYR cc_start: 0.7881 (m-80) cc_final: 0.7409 (m-80) REVERT: J 147 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5819 (pm20) REVERT: J 193 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: J 251 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7195 (mp0) REVERT: J 290 MET cc_start: 0.8904 (ttp) cc_final: 0.8473 (ttp) REVERT: J 297 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7830 (tm-30) REVERT: J 435 MET cc_start: 0.6124 (ttp) cc_final: 0.5878 (ttp) REVERT: K 34 CYS cc_start: 0.8005 (m) cc_final: 0.7758 (m) REVERT: K 46 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7408 (mm) REVERT: K 97 ARG cc_start: 0.8166 (mmt180) cc_final: 0.7876 (mmt180) REVERT: K 99 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7317 (tmtt) REVERT: K 115 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6358 (mt-10) REVERT: K 132 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8689 (mt) REVERT: K 147 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5330 (pm20) REVERT: K 194 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: K 235 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7206 (mt-10) REVERT: K 251 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7197 (mp0) REVERT: K 261 ASN cc_start: 0.6108 (m-40) cc_final: 0.5798 (m-40) REVERT: K 273 ILE cc_start: 0.8309 (mt) cc_final: 0.8100 (pt) REVERT: K 297 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7787 (tm-30) REVERT: K 326 LEU cc_start: 0.8295 (mp) cc_final: 0.7878 (mp) REVERT: L 34 CYS cc_start: 0.8193 (m) cc_final: 0.7985 (m) REVERT: L 46 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7341 (mm) REVERT: L 97 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7731 (mmt180) REVERT: L 147 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: L 179 MET cc_start: 0.7251 (tpt) cc_final: 0.6877 (tpt) REVERT: L 192 GLN cc_start: 0.8114 (mm110) cc_final: 0.7730 (mm-40) REVERT: L 194 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: L 251 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6995 (mp0) REVERT: L 253 PHE cc_start: 0.8722 (m-10) cc_final: 0.8511 (m-10) REVERT: L 270 GLN cc_start: 0.8242 (tp40) cc_final: 0.8014 (tp40) REVERT: L 274 ASP cc_start: 0.8631 (m-30) cc_final: 0.8359 (m-30) REVERT: L 297 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7916 (tm-30) REVERT: L 433 LEU cc_start: 0.8750 (mt) cc_final: 0.8536 (mt) REVERT: L 435 MET cc_start: 0.5918 (ttp) cc_final: 0.5307 (ttp) outliers start: 228 outliers final: 82 residues processed: 1379 average time/residue: 0.2531 time to fit residues: 557.6157 Evaluate side-chains 1133 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1002 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 111 GLN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 0.0570 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 106 GLN A 148 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN F 432 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN H 148 GLN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 GLN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 GLN J 82 ASN ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 148 GLN J 192 GLN K 11 GLN ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 148 GLN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123064 restraints weight = 59320.932| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.71 r_work: 0.3212 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 39972 Z= 0.216 Angle : 0.668 11.407 54132 Z= 0.341 Chirality : 0.047 0.203 6264 Planarity : 0.005 0.046 6972 Dihedral : 8.385 88.535 5709 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.81 % Allowed : 13.82 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.11), residues: 4944 helix: 0.95 (0.12), residues: 1632 sheet: -0.41 (0.14), residues: 1140 loop : -1.10 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 15 TYR 0.011 0.001 TYR J 337 PHE 0.025 0.002 PHE A 461 TRP 0.006 0.001 TRP K 125 HIS 0.008 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00508 (39948) covalent geometry : angle 0.66755 (54132) hydrogen bonds : bond 0.04116 ( 1801) hydrogen bonds : angle 4.97898 ( 4899) metal coordination : bond 0.00355 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 992 time to evaluate : 1.350 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: A 99 LYS cc_start: 0.7968 (tppp) cc_final: 0.7346 (tptt) REVERT: A 115 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 147 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: A 192 GLN cc_start: 0.7954 (mm110) cc_final: 0.6911 (mm110) REVERT: A 219 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7341 (mm) REVERT: A 227 SER cc_start: 0.8150 (m) cc_final: 0.7638 (t) REVERT: A 251 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7267 (mp0) REVERT: A 261 ASN cc_start: 0.6589 (t0) cc_final: 0.6030 (m-40) REVERT: A 265 CYS cc_start: 0.8436 (m) cc_final: 0.8223 (m) REVERT: A 297 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 326 LEU cc_start: 0.8647 (mp) cc_final: 0.8430 (mt) REVERT: A 372 ASN cc_start: 0.6233 (t0) cc_final: 0.5729 (t0) REVERT: A 384 GLU cc_start: 0.8136 (tp30) cc_final: 0.7881 (tp30) REVERT: A 417 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 19 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7957 (mtmm) REVERT: B 115 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 147 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5693 (pm20) REVERT: B 192 GLN cc_start: 0.7688 (mm110) cc_final: 0.7226 (mm110) REVERT: B 219 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7066 (mm) REVERT: B 227 SER cc_start: 0.7989 (m) cc_final: 0.7476 (t) REVERT: B 251 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7035 (mp0) REVERT: B 261 ASN cc_start: 0.6697 (t0) cc_final: 0.6164 (m-40) REVERT: B 273 ILE cc_start: 0.8561 (mt) cc_final: 0.8282 (pt) REVERT: B 297 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 326 LEU cc_start: 0.8403 (mp) cc_final: 0.8085 (mt) REVERT: B 364 HIS cc_start: 0.8092 (m-70) cc_final: 0.7800 (m170) REVERT: B 371 VAL cc_start: 0.8267 (t) cc_final: 0.8005 (m) REVERT: B 372 ASN cc_start: 0.6220 (t0) cc_final: 0.5684 (t0) REVERT: B 423 LEU cc_start: 0.9162 (tp) cc_final: 0.8946 (tt) REVERT: C 19 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8124 (mtmt) REVERT: C 97 ARG cc_start: 0.8391 (mmt180) cc_final: 0.7891 (mmt180) REVERT: C 147 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: C 219 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7631 (mm) REVERT: C 227 SER cc_start: 0.8174 (m) cc_final: 0.7737 (t) REVERT: C 250 TYR cc_start: 0.8374 (m-80) cc_final: 0.7887 (m-80) REVERT: C 251 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7248 (mp0) REVERT: C 261 ASN cc_start: 0.6613 (t0) cc_final: 0.6390 (m-40) REVERT: C 297 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 326 LEU cc_start: 0.8173 (mp) cc_final: 0.7909 (mt) REVERT: C 384 GLU cc_start: 0.8035 (tp30) cc_final: 0.7563 (tp30) REVERT: D 58 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7464 (p) REVERT: D 60 TYR cc_start: 0.8220 (m-80) cc_final: 0.7716 (m-80) REVERT: D 97 ARG cc_start: 0.8143 (mmt180) cc_final: 0.7791 (mmm-85) REVERT: D 147 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: D 179 MET cc_start: 0.7510 (tpt) cc_final: 0.7086 (tpt) REVERT: D 192 GLN cc_start: 0.7930 (mm110) cc_final: 0.7314 (mm-40) REVERT: D 251 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7277 (mp0) REVERT: D 261 ASN cc_start: 0.7092 (m-40) cc_final: 0.6834 (t0) REVERT: D 270 GLN cc_start: 0.8568 (tp40) cc_final: 0.8151 (tp40) REVERT: D 274 ASP cc_start: 0.8759 (m-30) cc_final: 0.8521 (m-30) REVERT: D 282 LEU cc_start: 0.8707 (tp) cc_final: 0.8455 (tp) REVERT: D 290 MET cc_start: 0.8821 (ttp) cc_final: 0.8589 (ttp) REVERT: D 326 LEU cc_start: 0.8170 (mp) cc_final: 0.7950 (mt) REVERT: D 371 VAL cc_start: 0.8208 (t) cc_final: 0.7991 (m) REVERT: D 372 ASN cc_start: 0.6034 (t0) cc_final: 0.5582 (t0) REVERT: D 398 LEU cc_start: 0.9034 (mp) cc_final: 0.8831 (mp) REVERT: E 46 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7323 (mm) REVERT: E 58 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7280 (p) REVERT: E 60 TYR cc_start: 0.8290 (m-80) cc_final: 0.7950 (m-80) REVERT: E 99 LYS cc_start: 0.8101 (tppp) cc_final: 0.7480 (tptp) REVERT: E 147 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: E 192 GLN cc_start: 0.7945 (mm110) cc_final: 0.7478 (mm-40) REVERT: E 219 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7791 (mm) REVERT: E 234 MET cc_start: 0.7642 (mtt) cc_final: 0.7246 (mmt) REVERT: E 235 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7266 (mt-10) REVERT: E 251 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 326 LEU cc_start: 0.8048 (mp) cc_final: 0.7747 (mp) REVERT: E 384 GLU cc_start: 0.7810 (tp30) cc_final: 0.7607 (tp30) REVERT: F 58 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7354 (p) REVERT: F 60 TYR cc_start: 0.8240 (m-80) cc_final: 0.7374 (m-80) REVERT: F 147 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5294 (pm20) REVERT: F 219 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7459 (mm) REVERT: F 251 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7347 (mp0) REVERT: F 261 ASN cc_start: 0.6476 (m-40) cc_final: 0.5554 (m-40) REVERT: F 265 CYS cc_start: 0.8550 (m) cc_final: 0.8317 (m) REVERT: F 274 ASP cc_start: 0.8916 (m-30) cc_final: 0.8527 (m-30) REVERT: F 295 ASP cc_start: 0.8976 (t0) cc_final: 0.8679 (t0) REVERT: F 297 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7998 (tm-30) REVERT: F 331 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7054 (mt-10) REVERT: F 371 VAL cc_start: 0.8498 (t) cc_final: 0.8277 (m) REVERT: F 372 ASN cc_start: 0.6100 (t0) cc_final: 0.5597 (t0) REVERT: F 417 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8172 (mp) REVERT: G 58 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7108 (p) REVERT: G 60 TYR cc_start: 0.8354 (m-80) cc_final: 0.7819 (m-80) REVERT: G 97 ARG cc_start: 0.8244 (mmt180) cc_final: 0.7824 (mmt180) REVERT: G 99 LYS cc_start: 0.8140 (tppp) cc_final: 0.7539 (tptt) REVERT: G 115 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6708 (tm-30) REVERT: G 127 ASP cc_start: 0.9084 (m-30) cc_final: 0.8839 (m-30) REVERT: G 147 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5976 (pm20) REVERT: G 219 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7435 (mm) REVERT: G 251 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7242 (mp0) REVERT: G 261 ASN cc_start: 0.6873 (t0) cc_final: 0.6486 (m-40) REVERT: G 274 ASP cc_start: 0.8780 (m-30) cc_final: 0.8196 (m-30) REVERT: G 371 VAL cc_start: 0.8458 (t) cc_final: 0.8143 (m) REVERT: G 372 ASN cc_start: 0.6241 (t0) cc_final: 0.5944 (t0) REVERT: G 389 GLU cc_start: 0.7937 (tp30) cc_final: 0.7671 (tp30) REVERT: G 432 GLN cc_start: 0.8857 (tt0) cc_final: 0.8487 (tt0) REVERT: G 460 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8211 (tt) REVERT: H 58 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.6880 (p) REVERT: H 60 TYR cc_start: 0.8263 (m-80) cc_final: 0.7376 (m-80) REVERT: H 82 ASN cc_start: 0.8587 (m-40) cc_final: 0.8134 (m-40) REVERT: H 147 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6393 (pt0) REVERT: H 192 GLN cc_start: 0.7939 (mm110) cc_final: 0.7502 (mm110) REVERT: H 227 SER cc_start: 0.8142 (m) cc_final: 0.7564 (t) REVERT: H 234 MET cc_start: 0.7602 (mtt) cc_final: 0.7337 (mtt) REVERT: H 251 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7314 (mp0) REVERT: H 261 ASN cc_start: 0.6324 (t0) cc_final: 0.5906 (m-40) REVERT: H 273 ILE cc_start: 0.8520 (pt) cc_final: 0.8270 (mt) REVERT: H 295 ASP cc_start: 0.8969 (t0) cc_final: 0.8762 (t0) REVERT: H 297 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7997 (tm-30) REVERT: H 326 LEU cc_start: 0.8585 (mp) cc_final: 0.8280 (mt) REVERT: H 345 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7232 (p-80) REVERT: H 365 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7572 (mtpp) REVERT: H 372 ASN cc_start: 0.5925 (t0) cc_final: 0.5665 (t0) REVERT: I 46 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7298 (mm) REVERT: I 97 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7756 (mmt-90) REVERT: I 99 LYS cc_start: 0.8040 (tppp) cc_final: 0.7835 (mmmt) REVERT: I 115 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6913 (tm-30) REVERT: I 139 LYS cc_start: 0.6106 (tmtt) cc_final: 0.5728 (tptp) REVERT: I 147 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: I 232 LEU cc_start: 0.8441 (mp) cc_final: 0.8203 (mp) REVERT: I 251 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7335 (mp0) REVERT: I 261 ASN cc_start: 0.6640 (t0) cc_final: 0.6268 (m-40) REVERT: I 297 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8044 (tm-30) REVERT: I 326 LEU cc_start: 0.8296 (mp) cc_final: 0.8022 (mt) REVERT: I 331 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7062 (mt-10) REVERT: I 360 ARG cc_start: 0.4995 (mtp180) cc_final: 0.3634 (ptp-170) REVERT: I 365 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7760 (mtpp) REVERT: I 459 GLU cc_start: 0.7748 (pp20) cc_final: 0.7511 (pp20) REVERT: I 460 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8250 (tp) REVERT: J 23 ARG cc_start: 0.7293 (ptt180) cc_final: 0.6674 (ptt180) REVERT: J 46 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7460 (mm) REVERT: J 58 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7168 (p) REVERT: J 60 TYR cc_start: 0.8228 (m-80) cc_final: 0.7633 (m-80) REVERT: J 97 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7795 (mmt180) REVERT: J 147 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5414 (pm20) REVERT: J 251 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7227 (mp0) REVERT: J 261 ASN cc_start: 0.6722 (m-40) cc_final: 0.5996 (t0) REVERT: J 265 CYS cc_start: 0.8656 (m) cc_final: 0.8405 (m) REVERT: J 290 MET cc_start: 0.8910 (ttp) cc_final: 0.8572 (ttp) REVERT: J 297 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7964 (tm-30) REVERT: K 34 CYS cc_start: 0.8252 (m) cc_final: 0.8021 (m) REVERT: K 46 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7546 (mm) REVERT: K 58 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7611 (p) REVERT: K 99 LYS cc_start: 0.8057 (tppp) cc_final: 0.7561 (ttmm) REVERT: K 115 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6293 (mt-10) REVERT: K 147 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5630 (pm20) REVERT: K 189 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7241 (t) REVERT: K 192 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7604 (mm-40) REVERT: K 193 GLU cc_start: 0.7768 (pt0) cc_final: 0.7268 (pt0) REVERT: K 251 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7245 (mp0) REVERT: K 261 ASN cc_start: 0.6522 (t0) cc_final: 0.6306 (m-40) REVERT: K 273 ILE cc_start: 0.8450 (mt) cc_final: 0.8248 (pt) REVERT: K 297 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8053 (tm-30) REVERT: K 326 LEU cc_start: 0.8425 (mp) cc_final: 0.7965 (mp) REVERT: K 343 MET cc_start: 0.8453 (mmm) cc_final: 0.8141 (mmm) REVERT: K 371 VAL cc_start: 0.8590 (t) cc_final: 0.8361 (m) REVERT: K 417 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8359 (mt) REVERT: L 34 CYS cc_start: 0.8415 (m) cc_final: 0.8180 (m) REVERT: L 46 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7443 (mm) REVERT: L 58 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.6901 (p) REVERT: L 60 TYR cc_start: 0.8156 (m-80) cc_final: 0.7213 (m-80) REVERT: L 179 MET cc_start: 0.7267 (tpt) cc_final: 0.7039 (tpt) REVERT: L 192 GLN cc_start: 0.7896 (mm110) cc_final: 0.7654 (mm-40) REVERT: L 219 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (mm) REVERT: L 251 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7142 (mp0) REVERT: L 253 PHE cc_start: 0.8945 (m-80) cc_final: 0.8672 (m-10) REVERT: L 297 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8312 (tm-30) outliers start: 206 outliers final: 121 residues processed: 1128 average time/residue: 0.2412 time to fit residues: 443.1205 Evaluate side-chains 1068 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 909 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 426 LEU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 201 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 491 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 493 optimal weight: 0.9980 chunk 467 optimal weight: 2.9990 chunk 385 optimal weight: 4.9990 chunk 365 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS C 192 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 GLN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN K 40 GLN ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN L 40 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127151 restraints weight = 60020.841| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.80 r_work: 0.3254 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39972 Z= 0.121 Angle : 0.587 8.319 54132 Z= 0.300 Chirality : 0.045 0.254 6264 Planarity : 0.005 0.037 6972 Dihedral : 6.160 55.114 5563 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.15 % Allowed : 16.06 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.11), residues: 4944 helix: 1.09 (0.12), residues: 1644 sheet: -0.43 (0.15), residues: 1140 loop : -1.10 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 388 TYR 0.009 0.001 TYR F 117 PHE 0.017 0.001 PHE A 461 TRP 0.005 0.001 TRP B 122 HIS 0.007 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00279 (39948) covalent geometry : angle 0.58728 (54132) hydrogen bonds : bond 0.03439 ( 1801) hydrogen bonds : angle 4.72252 ( 4899) metal coordination : bond 0.00062 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1015 time to evaluate : 1.488 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: A 23 ARG cc_start: 0.7742 (ptt180) cc_final: 0.7487 (ptt-90) REVERT: A 55 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7587 (mtmm) REVERT: A 60 TYR cc_start: 0.8145 (m-80) cc_final: 0.7541 (m-80) REVERT: A 115 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6652 (tm-30) REVERT: A 219 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7139 (mm) REVERT: A 227 SER cc_start: 0.8102 (m) cc_final: 0.7591 (t) REVERT: A 251 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7234 (mp0) REVERT: A 261 ASN cc_start: 0.6927 (t0) cc_final: 0.5999 (m-40) REVERT: A 297 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 326 LEU cc_start: 0.8522 (mp) cc_final: 0.8305 (mt) REVERT: A 372 ASN cc_start: 0.6232 (t0) cc_final: 0.5712 (t0) REVERT: A 384 GLU cc_start: 0.7628 (tp30) cc_final: 0.7312 (tp30) REVERT: A 417 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 19 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7931 (mtmm) REVERT: B 115 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6823 (tm-30) REVERT: B 189 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7480 (t) REVERT: B 192 GLN cc_start: 0.7779 (mm110) cc_final: 0.7296 (mm110) REVERT: B 219 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7028 (mm) REVERT: B 251 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7102 (mp0) REVERT: B 261 ASN cc_start: 0.6687 (t0) cc_final: 0.6236 (m-40) REVERT: B 297 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 326 LEU cc_start: 0.8335 (mp) cc_final: 0.7997 (mt) REVERT: B 360 ARG cc_start: 0.5001 (mtp180) cc_final: 0.3707 (ptp-170) REVERT: B 371 VAL cc_start: 0.8186 (t) cc_final: 0.7963 (m) REVERT: B 372 ASN cc_start: 0.6196 (t0) cc_final: 0.5633 (t0) REVERT: B 384 GLU cc_start: 0.8261 (tp30) cc_final: 0.7947 (tp30) REVERT: B 432 GLN cc_start: 0.8669 (tt0) cc_final: 0.8087 (tt0) REVERT: C 97 ARG cc_start: 0.8276 (mmt180) cc_final: 0.7842 (mmt180) REVERT: C 192 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7342 (mm-40) REVERT: C 219 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7559 (mm) REVERT: C 227 SER cc_start: 0.8029 (m) cc_final: 0.7626 (t) REVERT: C 251 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7205 (mp0) REVERT: C 261 ASN cc_start: 0.6843 (t0) cc_final: 0.6483 (m-40) REVERT: C 297 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 326 LEU cc_start: 0.8147 (mp) cc_final: 0.7837 (mt) REVERT: C 363 PHE cc_start: 0.8731 (m-10) cc_final: 0.8517 (m-80) REVERT: C 384 GLU cc_start: 0.7609 (tp30) cc_final: 0.7195 (tp30) REVERT: C 388 ARG cc_start: 0.7000 (mtm180) cc_final: 0.6766 (mtm180) REVERT: D 7 LYS cc_start: 0.4595 (OUTLIER) cc_final: 0.3992 (pttm) REVERT: D 46 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7206 (mm) REVERT: D 58 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7405 (p) REVERT: D 60 TYR cc_start: 0.8096 (m-80) cc_final: 0.7535 (m-80) REVERT: D 97 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7816 (mmm160) REVERT: D 132 LEU cc_start: 0.8749 (mt) cc_final: 0.8492 (mp) REVERT: D 179 MET cc_start: 0.7464 (tpt) cc_final: 0.7107 (tpt) REVERT: D 192 GLN cc_start: 0.7932 (mm110) cc_final: 0.7317 (mm-40) REVERT: D 235 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7198 (mt-10) REVERT: D 251 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7210 (mp0) REVERT: D 253 PHE cc_start: 0.8850 (m-80) cc_final: 0.8538 (m-10) REVERT: D 270 GLN cc_start: 0.8435 (tp40) cc_final: 0.8232 (tp40) REVERT: D 274 ASP cc_start: 0.8715 (m-30) cc_final: 0.8509 (m-30) REVERT: D 282 LEU cc_start: 0.8752 (tp) cc_final: 0.8544 (tp) REVERT: D 326 LEU cc_start: 0.8084 (mp) cc_final: 0.7862 (mt) REVERT: D 372 ASN cc_start: 0.5826 (t0) cc_final: 0.5383 (t0) REVERT: E 46 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7133 (mm) REVERT: E 58 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7187 (p) REVERT: E 60 TYR cc_start: 0.8164 (m-80) cc_final: 0.7840 (m-80) REVERT: E 99 LYS cc_start: 0.8134 (tppp) cc_final: 0.7538 (tmtt) REVERT: E 219 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7551 (mm) REVERT: E 234 MET cc_start: 0.7572 (mtt) cc_final: 0.7262 (mmt) REVERT: E 297 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 326 LEU cc_start: 0.8035 (mp) cc_final: 0.7685 (mp) REVERT: F 23 ARG cc_start: 0.7565 (ptt180) cc_final: 0.7341 (ptt180) REVERT: F 58 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7293 (p) REVERT: F 60 TYR cc_start: 0.8038 (m-80) cc_final: 0.7370 (m-80) REVERT: F 128 ARG cc_start: 0.9041 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: F 219 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7262 (mm) REVERT: F 251 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7327 (mp0) REVERT: F 274 ASP cc_start: 0.8858 (m-30) cc_final: 0.8481 (m-30) REVERT: F 297 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 331 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6998 (mt-10) REVERT: F 371 VAL cc_start: 0.8448 (t) cc_final: 0.8238 (m) REVERT: F 372 ASN cc_start: 0.6026 (t0) cc_final: 0.5554 (t0) REVERT: F 384 GLU cc_start: 0.8058 (tp30) cc_final: 0.7750 (tp30) REVERT: F 417 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8090 (mp) REVERT: F 440 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6419 (mt-10) REVERT: G 50 GLU cc_start: 0.7769 (tp30) cc_final: 0.7538 (mm-30) REVERT: G 58 SER cc_start: 0.7634 (OUTLIER) cc_final: 0.7029 (p) REVERT: G 60 TYR cc_start: 0.8259 (m-80) cc_final: 0.7724 (m-80) REVERT: G 99 LYS cc_start: 0.8049 (tppp) cc_final: 0.7478 (tptt) REVERT: G 115 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6707 (tm-30) REVERT: G 193 GLU cc_start: 0.7642 (pt0) cc_final: 0.7410 (pt0) REVERT: G 219 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7348 (mm) REVERT: G 251 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7107 (mp0) REVERT: G 274 ASP cc_start: 0.8802 (m-30) cc_final: 0.8272 (m-30) REVERT: G 371 VAL cc_start: 0.8456 (t) cc_final: 0.8182 (m) REVERT: G 372 ASN cc_start: 0.6233 (t0) cc_final: 0.5885 (t0) REVERT: G 460 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (tt) REVERT: H 58 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.6965 (p) REVERT: H 60 TYR cc_start: 0.8157 (m-80) cc_final: 0.7467 (m-80) REVERT: H 82 ASN cc_start: 0.8610 (m-40) cc_final: 0.8158 (m-40) REVERT: H 99 LYS cc_start: 0.7829 (ttmm) cc_final: 0.6915 (tptp) REVERT: H 189 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7432 (t) REVERT: H 192 GLN cc_start: 0.7995 (mm110) cc_final: 0.7093 (mm110) REVERT: H 227 SER cc_start: 0.8047 (m) cc_final: 0.7499 (t) REVERT: H 234 MET cc_start: 0.7655 (mtt) cc_final: 0.7417 (mtt) REVERT: H 251 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7388 (mp0) REVERT: H 297 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7732 (tm-30) REVERT: H 326 LEU cc_start: 0.8537 (mp) cc_final: 0.8200 (mt) REVERT: H 345 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7276 (p-80) REVERT: H 372 ASN cc_start: 0.5892 (t0) cc_final: 0.5597 (t0) REVERT: I 7 LYS cc_start: 0.4226 (OUTLIER) cc_final: 0.3538 (pttm) REVERT: I 46 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7290 (mm) REVERT: I 99 LYS cc_start: 0.7948 (tppp) cc_final: 0.7731 (mmmt) REVERT: I 115 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6684 (tm-30) REVERT: I 139 LYS cc_start: 0.6183 (tmtt) cc_final: 0.5942 (tptp) REVERT: I 251 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7268 (mp0) REVERT: I 261 ASN cc_start: 0.6894 (t0) cc_final: 0.6491 (m-40) REVERT: I 297 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7908 (tm-30) REVERT: I 326 LEU cc_start: 0.8313 (mp) cc_final: 0.8028 (mt) REVERT: I 331 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7014 (mt-10) REVERT: I 360 ARG cc_start: 0.5055 (mtp180) cc_final: 0.3667 (ptp-170) REVERT: I 386 LEU cc_start: 0.8407 (mm) cc_final: 0.8193 (mp) REVERT: I 459 GLU cc_start: 0.7764 (pp20) cc_final: 0.7535 (pp20) REVERT: I 460 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8258 (tp) REVERT: J 23 ARG cc_start: 0.7246 (ptt180) cc_final: 0.6781 (ptt180) REVERT: J 46 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7375 (mm) REVERT: J 58 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7378 (p) REVERT: J 60 TYR cc_start: 0.8145 (m-80) cc_final: 0.7594 (m-80) REVERT: J 97 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7738 (mmt180) REVERT: J 192 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7439 (mm110) REVERT: J 251 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7191 (mp0) REVERT: J 261 ASN cc_start: 0.6674 (m-40) cc_final: 0.5844 (t0) REVERT: J 265 CYS cc_start: 0.8679 (m) cc_final: 0.8459 (m) REVERT: J 297 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8014 (tm-30) REVERT: K 15 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6838 (mmt180) REVERT: K 34 CYS cc_start: 0.8428 (m) cc_final: 0.8217 (m) REVERT: K 46 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7329 (mm) REVERT: K 99 LYS cc_start: 0.7970 (tppp) cc_final: 0.7517 (ttmm) REVERT: K 115 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6464 (mt-10) REVERT: K 189 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.7283 (t) REVERT: K 192 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7752 (mm-40) REVERT: K 193 GLU cc_start: 0.7751 (pt0) cc_final: 0.7503 (pt0) REVERT: K 232 LEU cc_start: 0.8735 (mp) cc_final: 0.8343 (mp) REVERT: K 251 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7255 (mp0) REVERT: K 297 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7929 (tm-30) REVERT: K 326 LEU cc_start: 0.8460 (mp) cc_final: 0.7988 (mp) REVERT: K 371 VAL cc_start: 0.8623 (t) cc_final: 0.8417 (m) REVERT: K 388 ARG cc_start: 0.7197 (mtp85) cc_final: 0.6958 (mtp180) REVERT: K 417 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (mp) REVERT: L 34 CYS cc_start: 0.8432 (m) cc_final: 0.8183 (m) REVERT: L 46 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7381 (mm) REVERT: L 58 SER cc_start: 0.7594 (OUTLIER) cc_final: 0.7054 (p) REVERT: L 60 TYR cc_start: 0.8049 (m-80) cc_final: 0.7221 (m-80) REVERT: L 97 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7898 (mmt180) REVERT: L 128 ARG cc_start: 0.9113 (mmt-90) cc_final: 0.8721 (mmt180) REVERT: L 179 MET cc_start: 0.7466 (tpt) cc_final: 0.7217 (tpt) REVERT: L 192 GLN cc_start: 0.7981 (mm110) cc_final: 0.7657 (mm-40) REVERT: L 219 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7463 (mm) REVERT: L 232 LEU cc_start: 0.7983 (mp) cc_final: 0.7700 (mp) REVERT: L 251 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7084 (mp0) REVERT: L 297 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8024 (tm-30) REVERT: L 384 GLU cc_start: 0.7816 (tp30) cc_final: 0.7578 (tp30) outliers start: 178 outliers final: 110 residues processed: 1133 average time/residue: 0.2381 time to fit residues: 439.8263 Evaluate side-chains 1062 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 921 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 42 optimal weight: 10.0000 chunk 402 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 395 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN C 148 GLN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN H 65 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 65 ASN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN L 11 GLN L 40 GLN L 111 GLN ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124270 restraints weight = 59950.813| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.77 r_work: 0.3227 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39972 Z= 0.172 Angle : 0.611 11.795 54132 Z= 0.311 Chirality : 0.045 0.230 6264 Planarity : 0.004 0.037 6972 Dihedral : 5.700 53.620 5509 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.95 % Allowed : 17.23 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 4944 helix: 1.04 (0.12), residues: 1632 sheet: -0.46 (0.14), residues: 1140 loop : -1.12 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 15 TYR 0.010 0.001 TYR F 117 PHE 0.022 0.002 PHE L 461 TRP 0.006 0.001 TRP K 52 HIS 0.008 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00404 (39948) covalent geometry : angle 0.61070 (54132) hydrogen bonds : bond 0.03536 ( 1801) hydrogen bonds : angle 4.74792 ( 4899) metal coordination : bond 0.00192 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 938 time to evaluate : 1.566 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: A 23 ARG cc_start: 0.7745 (ptt180) cc_final: 0.7518 (ptt-90) REVERT: A 55 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7613 (mtmm) REVERT: A 60 TYR cc_start: 0.8219 (m-80) cc_final: 0.7540 (m-80) REVERT: A 99 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7437 (tptt) REVERT: A 115 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 192 GLN cc_start: 0.7897 (mm-40) cc_final: 0.6866 (mm110) REVERT: A 219 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7175 (mm) REVERT: A 227 SER cc_start: 0.8113 (m) cc_final: 0.7619 (t) REVERT: A 251 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7248 (mp0) REVERT: A 261 ASN cc_start: 0.6633 (t0) cc_final: 0.5959 (m-40) REVERT: A 297 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 325 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7106 (t-170) REVERT: A 372 ASN cc_start: 0.6290 (t0) cc_final: 0.5725 (t0) REVERT: A 384 GLU cc_start: 0.7610 (tp30) cc_final: 0.7253 (tp30) REVERT: A 386 LEU cc_start: 0.8603 (mm) cc_final: 0.8397 (mp) REVERT: A 417 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 7 LYS cc_start: 0.4299 (OUTLIER) cc_final: 0.3834 (pttm) REVERT: B 106 GLN cc_start: 0.8027 (mm110) cc_final: 0.7241 (mm-40) REVERT: B 115 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6800 (tm-30) REVERT: B 189 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (t) REVERT: B 192 GLN cc_start: 0.7854 (mm110) cc_final: 0.7342 (mm110) REVERT: B 219 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7036 (mm) REVERT: B 227 SER cc_start: 0.7862 (m) cc_final: 0.7374 (t) REVERT: B 234 MET cc_start: 0.7585 (mmt) cc_final: 0.6973 (mmt) REVERT: B 251 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7112 (mp0) REVERT: B 261 ASN cc_start: 0.6650 (t0) cc_final: 0.6153 (m-40) REVERT: B 297 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 326 LEU cc_start: 0.8333 (mp) cc_final: 0.7991 (mt) REVERT: B 360 ARG cc_start: 0.4884 (mtp180) cc_final: 0.3184 (mtt-85) REVERT: B 371 VAL cc_start: 0.8266 (t) cc_final: 0.8030 (m) REVERT: B 372 ASN cc_start: 0.6290 (t0) cc_final: 0.5699 (t0) REVERT: B 384 GLU cc_start: 0.8211 (tp30) cc_final: 0.7867 (tp30) REVERT: B 388 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6783 (mtp180) REVERT: B 440 GLU cc_start: 0.6677 (tt0) cc_final: 0.6132 (tt0) REVERT: C 192 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7246 (mm-40) REVERT: C 227 SER cc_start: 0.8072 (m) cc_final: 0.7665 (t) REVERT: C 251 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7253 (mp0) REVERT: C 261 ASN cc_start: 0.6963 (t0) cc_final: 0.6601 (m-40) REVERT: C 297 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 326 LEU cc_start: 0.8134 (mp) cc_final: 0.7824 (mt) REVERT: C 384 GLU cc_start: 0.7726 (tp30) cc_final: 0.7148 (tp30) REVERT: C 388 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6739 (mtm180) REVERT: C 440 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6609 (tt0) REVERT: D 46 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7254 (mm) REVERT: D 58 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7474 (p) REVERT: D 60 TYR cc_start: 0.8182 (m-80) cc_final: 0.7574 (m-80) REVERT: D 97 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7847 (mmm160) REVERT: D 179 MET cc_start: 0.7427 (tpt) cc_final: 0.7037 (tpt) REVERT: D 192 GLN cc_start: 0.7986 (mm110) cc_final: 0.7302 (mm-40) REVERT: D 251 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7257 (mp0) REVERT: D 253 PHE cc_start: 0.8887 (m-80) cc_final: 0.8539 (m-10) REVERT: D 282 LEU cc_start: 0.8650 (tp) cc_final: 0.8425 (tp) REVERT: D 326 LEU cc_start: 0.8208 (mp) cc_final: 0.7949 (mt) REVERT: D 360 ARG cc_start: 0.5143 (mtp180) cc_final: 0.3010 (mtt-85) REVERT: D 372 ASN cc_start: 0.5859 (t0) cc_final: 0.5542 (t0) REVERT: E 19 LYS cc_start: 0.8241 (mtmm) cc_final: 0.8030 (mtmm) REVERT: E 46 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7112 (mm) REVERT: E 58 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.7191 (p) REVERT: E 60 TYR cc_start: 0.8251 (m-80) cc_final: 0.7909 (m-80) REVERT: E 99 LYS cc_start: 0.8142 (tppp) cc_final: 0.7527 (tptp) REVERT: E 219 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7609 (mm) REVERT: E 234 MET cc_start: 0.7394 (mtt) cc_final: 0.7082 (mmt) REVERT: E 297 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7736 (tm-30) REVERT: E 326 LEU cc_start: 0.8134 (mp) cc_final: 0.7794 (mp) REVERT: E 398 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (mp) REVERT: E 440 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6280 (tt0) REVERT: F 7 LYS cc_start: 0.4417 (OUTLIER) cc_final: 0.3980 (pttm) REVERT: F 58 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7339 (p) REVERT: F 60 TYR cc_start: 0.8197 (m-80) cc_final: 0.7358 (m-80) REVERT: F 115 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6331 (tm-30) REVERT: F 251 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7333 (mp0) REVERT: F 261 ASN cc_start: 0.6402 (t0) cc_final: 0.5986 (m-40) REVERT: F 297 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7850 (tm-30) REVERT: F 331 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7036 (mt-10) REVERT: F 371 VAL cc_start: 0.8490 (t) cc_final: 0.8266 (m) REVERT: F 372 ASN cc_start: 0.6248 (t0) cc_final: 0.5804 (t0) REVERT: F 417 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8185 (mp) REVERT: F 440 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6356 (mt-10) REVERT: G 50 GLU cc_start: 0.7779 (tp30) cc_final: 0.7532 (mm-30) REVERT: G 58 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7109 (p) REVERT: G 60 TYR cc_start: 0.8319 (m-80) cc_final: 0.7761 (m-80) REVERT: G 115 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6683 (tm-30) REVERT: G 192 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7371 (mm-40) REVERT: G 193 GLU cc_start: 0.7531 (pt0) cc_final: 0.7294 (pt0) REVERT: G 219 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (mm) REVERT: G 251 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7201 (mp0) REVERT: G 274 ASP cc_start: 0.8836 (m-30) cc_final: 0.8288 (m-30) REVERT: G 371 VAL cc_start: 0.8507 (t) cc_final: 0.8207 (m) REVERT: G 372 ASN cc_start: 0.6235 (t0) cc_final: 0.5888 (t0) REVERT: G 440 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: H 58 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7066 (p) REVERT: H 60 TYR cc_start: 0.8202 (m-80) cc_final: 0.7474 (m-80) REVERT: H 82 ASN cc_start: 0.8576 (m-40) cc_final: 0.8131 (m-40) REVERT: H 189 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7427 (t) REVERT: H 227 SER cc_start: 0.8046 (m) cc_final: 0.7501 (t) REVERT: H 251 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7405 (mp0) REVERT: H 297 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7747 (tm-30) REVERT: H 326 LEU cc_start: 0.8441 (mp) cc_final: 0.8079 (mt) REVERT: H 372 ASN cc_start: 0.6029 (t0) cc_final: 0.5655 (t0) REVERT: H 432 GLN cc_start: 0.8960 (tt0) cc_final: 0.8097 (tt0) REVERT: I 46 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7297 (mm) REVERT: I 99 LYS cc_start: 0.7948 (tppp) cc_final: 0.7741 (mmmt) REVERT: I 115 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6703 (tm-30) REVERT: I 139 LYS cc_start: 0.6126 (tmtt) cc_final: 0.5877 (tptp) REVERT: I 251 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7287 (mp0) REVERT: I 261 ASN cc_start: 0.6861 (t0) cc_final: 0.6512 (m-40) REVERT: I 297 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7847 (tm-30) REVERT: I 326 LEU cc_start: 0.8381 (mp) cc_final: 0.8089 (mt) REVERT: I 331 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7018 (mt-10) REVERT: I 360 ARG cc_start: 0.4928 (mtp180) cc_final: 0.3080 (mtt90) REVERT: I 365 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7321 (mtpp) REVERT: I 384 GLU cc_start: 0.7889 (tp30) cc_final: 0.7609 (tp30) REVERT: I 440 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: I 459 GLU cc_start: 0.7729 (pp20) cc_final: 0.7478 (pp20) REVERT: I 460 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8342 (tp) REVERT: J 23 ARG cc_start: 0.7317 (ptt180) cc_final: 0.6870 (ptt180) REVERT: J 46 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7351 (mm) REVERT: J 58 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7324 (p) REVERT: J 60 TYR cc_start: 0.8210 (m-80) cc_final: 0.7561 (m-80) REVERT: J 192 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7467 (mm110) REVERT: J 235 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7289 (mt-10) REVERT: J 251 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7210 (mp0) REVERT: J 261 ASN cc_start: 0.6725 (m-40) cc_final: 0.5934 (t0) REVERT: J 265 CYS cc_start: 0.8671 (m) cc_final: 0.8459 (m) REVERT: J 297 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8054 (tm-30) REVERT: K 21 VAL cc_start: 0.9378 (m) cc_final: 0.9123 (t) REVERT: K 99 LYS cc_start: 0.7980 (tppp) cc_final: 0.7561 (ttmm) REVERT: K 115 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6494 (mt-10) REVERT: K 189 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7399 (t) REVERT: K 192 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7716 (mm-40) REVERT: K 193 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: K 251 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7278 (mp0) REVERT: K 290 MET cc_start: 0.8774 (ttp) cc_final: 0.8523 (ttm) REVERT: K 297 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7828 (tm-30) REVERT: K 326 LEU cc_start: 0.8436 (mp) cc_final: 0.8012 (mp) REVERT: K 371 VAL cc_start: 0.8618 (t) cc_final: 0.8397 (m) REVERT: K 417 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8258 (mp) REVERT: K 440 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6300 (tt0) REVERT: L 34 CYS cc_start: 0.8440 (m) cc_final: 0.8204 (m) REVERT: L 46 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7428 (mm) REVERT: L 58 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7156 (p) REVERT: L 60 TYR cc_start: 0.8118 (m-80) cc_final: 0.7342 (m-80) REVERT: L 97 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7962 (mmt180) REVERT: L 115 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6599 (tm-30) REVERT: L 128 ARG cc_start: 0.9118 (mmt-90) cc_final: 0.8762 (mmt180) REVERT: L 192 GLN cc_start: 0.8001 (mm110) cc_final: 0.7652 (mm-40) REVERT: L 219 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7403 (mm) REVERT: L 232 LEU cc_start: 0.7991 (mp) cc_final: 0.7702 (mp) REVERT: L 234 MET cc_start: 0.7115 (mmt) cc_final: 0.6808 (mmt) REVERT: L 251 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7122 (mp0) REVERT: L 297 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 212 outliers final: 143 residues processed: 1074 average time/residue: 0.2478 time to fit residues: 433.8767 Evaluate side-chains 1069 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 893 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 193 GLU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 371 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 411 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 268 optimal weight: 0.7980 chunk 279 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN L 40 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 GLN ** 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 = 0.3588 r_free = 0.3588 target = 0.142326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121524 restraints weight = 59917.830| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.86 r_work: 0.3224 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39972 Z= 0.146 Angle : 0.587 13.505 54132 Z= 0.299 Chirality : 0.045 0.221 6264 Planarity : 0.004 0.035 6972 Dihedral : 5.500 52.651 5502 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.35 % Allowed : 18.46 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 4944 helix: 1.04 (0.12), residues: 1632 sheet: -0.47 (0.14), residues: 1140 loop : -1.11 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 15 TYR 0.009 0.001 TYR F 117 PHE 0.026 0.002 PHE L 461 TRP 0.006 0.001 TRP I 122 HIS 0.008 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00344 (39948) covalent geometry : angle 0.58745 (54132) hydrogen bonds : bond 0.03375 ( 1801) hydrogen bonds : angle 4.70958 ( 4899) metal coordination : bond 0.00135 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 953 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: A 55 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7571 (mtmm) REVERT: A 60 TYR cc_start: 0.8180 (m-80) cc_final: 0.7522 (m-80) REVERT: A 99 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7435 (tptt) REVERT: A 115 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6646 (tm-30) REVERT: A 189 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7313 (t) REVERT: A 192 GLN cc_start: 0.7855 (mm-40) cc_final: 0.6811 (mm110) REVERT: A 219 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7230 (mm) REVERT: A 227 SER cc_start: 0.8064 (m) cc_final: 0.7573 (t) REVERT: A 251 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7227 (mp0) REVERT: A 261 ASN cc_start: 0.6558 (t0) cc_final: 0.5965 (m-40) REVERT: A 274 ASP cc_start: 0.8931 (m-30) cc_final: 0.8549 (m-30) REVERT: A 289 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8293 (mtt180) REVERT: A 297 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 325 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.7063 (t-170) REVERT: A 372 ASN cc_start: 0.6425 (t0) cc_final: 0.5838 (t0) REVERT: A 417 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 440 GLU cc_start: 0.6708 (mt-10) cc_final: 0.5795 (tt0) REVERT: B 7 LYS cc_start: 0.4263 (OUTLIER) cc_final: 0.3768 (pttm) REVERT: B 99 LYS cc_start: 0.7441 (tppp) cc_final: 0.6653 (tptp) REVERT: B 115 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6663 (tm-30) REVERT: B 189 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 192 GLN cc_start: 0.7783 (mm110) cc_final: 0.7248 (mm110) REVERT: B 227 SER cc_start: 0.7763 (m) cc_final: 0.7269 (t) REVERT: B 234 MET cc_start: 0.7542 (mmt) cc_final: 0.6928 (mmt) REVERT: B 251 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7142 (mp0) REVERT: B 289 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: B 297 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 326 LEU cc_start: 0.8379 (mp) cc_final: 0.8039 (mt) REVERT: B 360 ARG cc_start: 0.4820 (mtp180) cc_final: 0.3160 (mtt-85) REVERT: B 371 VAL cc_start: 0.8303 (t) cc_final: 0.8087 (m) REVERT: B 372 ASN cc_start: 0.6291 (t0) cc_final: 0.5690 (t0) REVERT: B 384 GLU cc_start: 0.8097 (tp30) cc_final: 0.7850 (tp30) REVERT: B 388 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7003 (mtm180) REVERT: B 427 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7739 (t0) REVERT: B 440 GLU cc_start: 0.6640 (tt0) cc_final: 0.6083 (tt0) REVERT: C 19 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8149 (mtmt) REVERT: C 97 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8255 (mmt180) REVERT: C 192 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7245 (mm-40) REVERT: C 219 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7664 (mm) REVERT: C 227 SER cc_start: 0.8038 (m) cc_final: 0.7634 (t) REVERT: C 251 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7251 (mp0) REVERT: C 261 ASN cc_start: 0.6777 (t0) cc_final: 0.6381 (m-40) REVERT: C 297 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 326 LEU cc_start: 0.8173 (mp) cc_final: 0.7838 (mt) REVERT: C 384 GLU cc_start: 0.7756 (tp30) cc_final: 0.7095 (tp30) REVERT: C 388 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6657 (mtm180) REVERT: D 23 ARG cc_start: 0.7449 (ptt-90) cc_final: 0.7215 (ptt180) REVERT: D 46 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7178 (mm) REVERT: D 58 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7421 (p) REVERT: D 60 TYR cc_start: 0.8134 (m-80) cc_final: 0.7464 (m-80) REVERT: D 97 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7916 (mmm160) REVERT: D 128 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8826 (mmt-90) REVERT: D 179 MET cc_start: 0.7319 (tpt) cc_final: 0.6988 (tpt) REVERT: D 192 GLN cc_start: 0.7899 (mm110) cc_final: 0.7209 (mm-40) REVERT: D 235 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 251 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7253 (mp0) REVERT: D 253 PHE cc_start: 0.8857 (m-80) cc_final: 0.8458 (m-80) REVERT: D 270 GLN cc_start: 0.8559 (tp40) cc_final: 0.8192 (tp40) REVERT: D 289 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7770 (mtt180) REVERT: D 326 LEU cc_start: 0.8294 (mp) cc_final: 0.8008 (mt) REVERT: D 360 ARG cc_start: 0.4963 (mtp180) cc_final: 0.2966 (mtt-85) REVERT: D 372 ASN cc_start: 0.5716 (t0) cc_final: 0.5420 (t0) REVERT: E 7 LYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4564 (pttm) REVERT: E 46 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7062 (mm) REVERT: E 58 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7225 (p) REVERT: E 60 TYR cc_start: 0.8197 (m-80) cc_final: 0.7903 (m-80) REVERT: E 99 LYS cc_start: 0.8091 (tppp) cc_final: 0.7450 (tptp) REVERT: E 234 MET cc_start: 0.7441 (mtt) cc_final: 0.7027 (mmt) REVERT: E 297 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7722 (tm-30) REVERT: E 326 LEU cc_start: 0.8137 (mp) cc_final: 0.7885 (mt) REVERT: E 384 GLU cc_start: 0.7958 (tp30) cc_final: 0.7609 (tp30) REVERT: E 460 LEU cc_start: 0.8589 (tp) cc_final: 0.8353 (tt) REVERT: F 7 LYS cc_start: 0.4339 (OUTLIER) cc_final: 0.4046 (pttm) REVERT: F 23 ARG cc_start: 0.7654 (ptt180) cc_final: 0.7446 (ptt-90) REVERT: F 58 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7245 (p) REVERT: F 60 TYR cc_start: 0.8121 (m-80) cc_final: 0.7297 (m-80) REVERT: F 128 ARG cc_start: 0.9048 (mmt-90) cc_final: 0.8655 (mmt180) REVERT: F 139 LYS cc_start: 0.5536 (tptp) cc_final: 0.5270 (tptp) REVERT: F 219 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7232 (mm) REVERT: F 251 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7288 (mp0) REVERT: F 274 ASP cc_start: 0.8902 (m-30) cc_final: 0.8495 (m-30) REVERT: F 295 ASP cc_start: 0.8898 (t0) cc_final: 0.8533 (t0) REVERT: F 297 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7855 (tm-30) REVERT: F 331 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6884 (mt-10) REVERT: F 371 VAL cc_start: 0.8493 (t) cc_final: 0.8277 (m) REVERT: F 372 ASN cc_start: 0.6286 (t0) cc_final: 0.5826 (t0) REVERT: F 384 GLU cc_start: 0.8124 (tp30) cc_final: 0.7896 (tp30) REVERT: F 417 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8090 (mp) REVERT: F 440 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6279 (mt-10) REVERT: G 58 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.6971 (p) REVERT: G 60 TYR cc_start: 0.8271 (m-80) cc_final: 0.7649 (m-80) REVERT: G 115 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6611 (tm-30) REVERT: G 192 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7304 (mm-40) REVERT: G 193 GLU cc_start: 0.7651 (pt0) cc_final: 0.7391 (pt0) REVERT: G 219 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7197 (mm) REVERT: G 251 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7174 (mp0) REVERT: G 261 ASN cc_start: 0.6791 (m-40) cc_final: 0.6491 (m-40) REVERT: G 371 VAL cc_start: 0.8563 (t) cc_final: 0.8278 (m) REVERT: G 372 ASN cc_start: 0.6275 (t0) cc_final: 0.5893 (t0) REVERT: G 440 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: H 23 ARG cc_start: 0.7732 (ptt180) cc_final: 0.7114 (ptt180) REVERT: H 58 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7048 (p) REVERT: H 60 TYR cc_start: 0.8203 (m-80) cc_final: 0.7487 (m-80) REVERT: H 82 ASN cc_start: 0.8540 (m-40) cc_final: 0.8102 (m-40) REVERT: H 99 LYS cc_start: 0.7919 (ttmm) cc_final: 0.6947 (tptp) REVERT: H 189 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7079 (t) REVERT: H 192 GLN cc_start: 0.7709 (mm-40) cc_final: 0.6810 (mm110) REVERT: H 227 SER cc_start: 0.7948 (m) cc_final: 0.7390 (t) REVERT: H 251 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7412 (mp0) REVERT: H 289 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7823 (mtt180) REVERT: H 296 ASN cc_start: 0.8896 (m110) cc_final: 0.8669 (m-40) REVERT: H 297 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7574 (tm-30) REVERT: H 326 LEU cc_start: 0.8458 (mp) cc_final: 0.8099 (mt) REVERT: H 372 ASN cc_start: 0.5959 (t0) cc_final: 0.5588 (t0) REVERT: H 427 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7811 (t0) REVERT: H 440 GLU cc_start: 0.6684 (tt0) cc_final: 0.6247 (tt0) REVERT: I 46 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7253 (mm) REVERT: I 99 LYS cc_start: 0.7928 (tppp) cc_final: 0.7702 (mmmt) REVERT: I 115 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6603 (tm-30) REVERT: I 139 LYS cc_start: 0.6079 (tmtt) cc_final: 0.5829 (tptp) REVERT: I 227 SER cc_start: 0.7962 (m) cc_final: 0.7385 (t) REVERT: I 251 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7265 (mp0) REVERT: I 261 ASN cc_start: 0.6809 (t0) cc_final: 0.6479 (m-40) REVERT: I 297 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7774 (tm-30) REVERT: I 326 LEU cc_start: 0.8389 (mp) cc_final: 0.8088 (mt) REVERT: I 360 ARG cc_start: 0.4861 (mtp180) cc_final: 0.3087 (mtt90) REVERT: I 386 LEU cc_start: 0.8483 (mm) cc_final: 0.8268 (mp) REVERT: I 440 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6450 (tt0) REVERT: I 459 GLU cc_start: 0.7760 (pp20) cc_final: 0.7525 (pp20) REVERT: I 460 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8348 (tp) REVERT: J 23 ARG cc_start: 0.7373 (ptt180) cc_final: 0.6915 (ptt180) REVERT: J 46 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7296 (mm) REVERT: J 58 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7314 (p) REVERT: J 60 TYR cc_start: 0.8212 (m-80) cc_final: 0.7564 (m-80) REVERT: J 97 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7895 (mmt180) REVERT: J 251 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7237 (mp0) REVERT: J 265 CYS cc_start: 0.8634 (m) cc_final: 0.8430 (m) REVERT: J 290 MET cc_start: 0.8736 (ttp) cc_final: 0.8459 (ttp) REVERT: J 297 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7976 (tm-30) REVERT: K 21 VAL cc_start: 0.9346 (m) cc_final: 0.9130 (t) REVERT: K 99 LYS cc_start: 0.7959 (tppp) cc_final: 0.7573 (ttmm) REVERT: K 115 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6469 (mt-10) REVERT: K 192 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7680 (mm-40) REVERT: K 193 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: K 251 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7304 (mp0) REVERT: K 290 MET cc_start: 0.8790 (ttp) cc_final: 0.8541 (ttm) REVERT: K 297 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7609 (tm-30) REVERT: K 326 LEU cc_start: 0.8452 (mp) cc_final: 0.8024 (mp) REVERT: K 384 GLU cc_start: 0.7839 (tp30) cc_final: 0.7547 (tp30) REVERT: K 417 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8224 (mp) REVERT: K 427 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: K 440 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: L 34 CYS cc_start: 0.8414 (m) cc_final: 0.8185 (m) REVERT: L 46 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7276 (mm) REVERT: L 58 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7088 (p) REVERT: L 60 TYR cc_start: 0.8045 (m-80) cc_final: 0.7269 (m-80) REVERT: L 97 ARG cc_start: 0.8164 (mmt180) cc_final: 0.7930 (mmt180) REVERT: L 127 ASP cc_start: 0.8862 (m-30) cc_final: 0.8650 (m-30) REVERT: L 128 ARG cc_start: 0.9123 (mmt-90) cc_final: 0.8739 (mmt180) REVERT: L 139 LYS cc_start: 0.5570 (tptp) cc_final: 0.5282 (tptp) REVERT: L 192 GLN cc_start: 0.7991 (mm110) cc_final: 0.7645 (mm-40) REVERT: L 219 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7337 (mm) REVERT: L 232 LEU cc_start: 0.7944 (mp) cc_final: 0.7666 (mp) REVERT: L 251 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7125 (mp0) REVERT: L 297 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7791 (tm-30) REVERT: L 318 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8210 (mtp85) REVERT: L 364 HIS cc_start: 0.8132 (m-70) cc_final: 0.7880 (m-70) REVERT: L 384 GLU cc_start: 0.7763 (tp30) cc_final: 0.7477 (tp30) outliers start: 229 outliers final: 147 residues processed: 1103 average time/residue: 0.2307 time to fit residues: 414.9362 Evaluate side-chains 1077 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 891 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 GLU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 498 optimal weight: 2.9990 chunk 402 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 449 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 308 GLN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 296 ASN ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118072 restraints weight = 60855.401| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.86 r_work: 0.3175 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 39972 Z= 0.242 Angle : 0.676 12.137 54132 Z= 0.342 Chirality : 0.047 0.244 6264 Planarity : 0.005 0.035 6972 Dihedral : 5.790 50.639 5501 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.93 % Allowed : 18.79 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.11), residues: 4944 helix: 0.86 (0.12), residues: 1632 sheet: -0.54 (0.14), residues: 1140 loop : -1.17 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 15 TYR 0.013 0.002 TYR E 117 PHE 0.029 0.002 PHE L 461 TRP 0.007 0.001 TRP G 52 HIS 0.011 0.001 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00568 (39948) covalent geometry : angle 0.67625 (54132) hydrogen bonds : bond 0.03895 ( 1801) hydrogen bonds : angle 4.92159 ( 4899) metal coordination : bond 0.00289 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 916 time to evaluate : 1.391 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: A 7 LYS cc_start: 0.4307 (OUTLIER) cc_final: 0.3745 (pttm) REVERT: A 55 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7566 (mmtm) REVERT: A 115 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 219 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 227 SER cc_start: 0.8125 (m) cc_final: 0.7611 (t) REVERT: A 250 TYR cc_start: 0.8128 (m-80) cc_final: 0.7720 (m-80) REVERT: A 251 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7290 (mp0) REVERT: A 261 ASN cc_start: 0.6606 (t0) cc_final: 0.6312 (m-40) REVERT: A 289 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: A 297 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 325 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7179 (t-170) REVERT: A 372 ASN cc_start: 0.6510 (t0) cc_final: 0.5803 (t0) REVERT: A 386 LEU cc_start: 0.8592 (mm) cc_final: 0.8321 (mp) REVERT: A 417 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 440 GLU cc_start: 0.6881 (mt-10) cc_final: 0.5919 (tt0) REVERT: B 99 LYS cc_start: 0.7601 (tppp) cc_final: 0.6762 (tptp) REVERT: B 111 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: B 115 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6583 (tm-30) REVERT: B 189 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7471 (t) REVERT: B 192 GLN cc_start: 0.7674 (mm110) cc_final: 0.7148 (mm110) REVERT: B 219 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7021 (mm) REVERT: B 227 SER cc_start: 0.7883 (m) cc_final: 0.7387 (t) REVERT: B 251 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7216 (mp0) REVERT: B 261 ASN cc_start: 0.6641 (t0) cc_final: 0.6390 (m-40) REVERT: B 289 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7057 (mtt180) REVERT: B 297 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 326 LEU cc_start: 0.8405 (mp) cc_final: 0.8077 (mt) REVERT: B 360 ARG cc_start: 0.4672 (mtp180) cc_final: 0.3467 (mtt90) REVERT: B 372 ASN cc_start: 0.6452 (t0) cc_final: 0.5937 (t0) REVERT: B 384 GLU cc_start: 0.8127 (tp30) cc_final: 0.7897 (tp30) REVERT: B 388 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7213 (mtm180) REVERT: B 427 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7716 (t0) REVERT: B 440 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6183 (tt0) REVERT: C 192 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7302 (mm-40) REVERT: C 193 GLU cc_start: 0.7256 (pt0) cc_final: 0.6946 (pt0) REVERT: C 219 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7643 (mm) REVERT: C 227 SER cc_start: 0.8069 (m) cc_final: 0.7621 (t) REVERT: C 234 MET cc_start: 0.7432 (mmt) cc_final: 0.7027 (mmp) REVERT: C 251 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7330 (mp0) REVERT: C 261 ASN cc_start: 0.6273 (t0) cc_final: 0.5971 (m-40) REVERT: C 297 GLU cc_start: 0.8610 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 326 LEU cc_start: 0.8326 (mp) cc_final: 0.7984 (mt) REVERT: C 384 GLU cc_start: 0.7784 (tp30) cc_final: 0.7457 (tp30) REVERT: C 388 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6711 (mtm180) REVERT: C 440 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: D 58 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7434 (p) REVERT: D 60 TYR cc_start: 0.8243 (m-80) cc_final: 0.7729 (m-80) REVERT: D 97 ARG cc_start: 0.8251 (mmt180) cc_final: 0.7874 (mmm160) REVERT: D 179 MET cc_start: 0.7286 (tpt) cc_final: 0.6926 (tpt) REVERT: D 192 GLN cc_start: 0.7878 (mm110) cc_final: 0.7360 (mm-40) REVERT: D 251 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7318 (mp0) REVERT: D 253 PHE cc_start: 0.8917 (m-80) cc_final: 0.8540 (m-80) REVERT: D 326 LEU cc_start: 0.8409 (mp) cc_final: 0.8130 (mt) REVERT: D 343 MET cc_start: 0.8577 (mmm) cc_final: 0.8154 (mmm) REVERT: D 360 ARG cc_start: 0.4770 (mtp180) cc_final: 0.2899 (mtt-85) REVERT: D 372 ASN cc_start: 0.5738 (t0) cc_final: 0.5531 (t0) REVERT: E 15 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6503 (mmt180) REVERT: E 58 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7237 (p) REVERT: E 60 TYR cc_start: 0.8316 (m-80) cc_final: 0.8032 (m-80) REVERT: E 99 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7345 (tmtt) REVERT: E 219 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7738 (mm) REVERT: E 234 MET cc_start: 0.7353 (mtt) cc_final: 0.6885 (mmt) REVERT: E 297 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7983 (tm-30) REVERT: E 326 LEU cc_start: 0.8259 (mp) cc_final: 0.8017 (mt) REVERT: E 372 ASN cc_start: 0.6202 (t0) cc_final: 0.6001 (t0) REVERT: E 384 GLU cc_start: 0.7974 (tp30) cc_final: 0.7770 (tp30) REVERT: E 460 LEU cc_start: 0.8611 (tp) cc_final: 0.8396 (tt) REVERT: F 139 LYS cc_start: 0.5397 (tptp) cc_final: 0.5166 (tptp) REVERT: F 219 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7301 (mm) REVERT: F 234 MET cc_start: 0.7399 (mmt) cc_final: 0.6967 (mmt) REVERT: F 251 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7352 (mp0) REVERT: F 295 ASP cc_start: 0.8992 (t0) cc_final: 0.8791 (t0) REVERT: F 297 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7985 (tm-30) REVERT: F 331 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7006 (mt-10) REVERT: F 371 VAL cc_start: 0.8550 (t) cc_final: 0.8331 (m) REVERT: F 372 ASN cc_start: 0.6342 (t0) cc_final: 0.6121 (t0) REVERT: F 384 GLU cc_start: 0.8300 (tp30) cc_final: 0.7991 (tp30) REVERT: F 417 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8076 (mp) REVERT: F 440 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6497 (mt-10) REVERT: G 58 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7029 (p) REVERT: G 60 TYR cc_start: 0.8402 (m-80) cc_final: 0.7794 (m-80) REVERT: G 115 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6588 (tm-30) REVERT: G 127 ASP cc_start: 0.9136 (m-30) cc_final: 0.8911 (m-30) REVERT: G 192 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7411 (mm-40) REVERT: G 193 GLU cc_start: 0.7642 (pt0) cc_final: 0.7415 (pt0) REVERT: G 219 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7261 (mm) REVERT: G 251 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7315 (mp0) REVERT: G 289 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7970 (mtt180) REVERT: G 440 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: H 58 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.6922 (p) REVERT: H 60 TYR cc_start: 0.8276 (m-80) cc_final: 0.7449 (m-80) REVERT: H 82 ASN cc_start: 0.8579 (m-40) cc_final: 0.8138 (m-40) REVERT: H 99 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7148 (tptp) REVERT: H 227 SER cc_start: 0.8029 (m) cc_final: 0.7484 (t) REVERT: H 251 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7472 (mp0) REVERT: H 289 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7105 (mtt180) REVERT: H 297 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7662 (tm-30) REVERT: H 326 LEU cc_start: 0.8494 (mp) cc_final: 0.8175 (mt) REVERT: H 372 ASN cc_start: 0.6165 (t0) cc_final: 0.5698 (t0) REVERT: H 427 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7732 (t0) REVERT: H 440 GLU cc_start: 0.6708 (tt0) cc_final: 0.6249 (tt0) REVERT: I 46 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7343 (mm) REVERT: I 97 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7777 (mmt-90) REVERT: I 99 LYS cc_start: 0.7956 (tppp) cc_final: 0.7707 (mmmt) REVERT: I 115 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6630 (tm-30) REVERT: I 139 LYS cc_start: 0.6024 (tmtt) cc_final: 0.5751 (tptp) REVERT: I 251 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7310 (mp0) REVERT: I 261 ASN cc_start: 0.6709 (t0) cc_final: 0.6344 (m-40) REVERT: I 289 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (mtm-85) REVERT: I 297 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7799 (tm-30) REVERT: I 326 LEU cc_start: 0.8367 (mp) cc_final: 0.8062 (mt) REVERT: I 360 ARG cc_start: 0.4735 (mtp180) cc_final: 0.3025 (mtt90) REVERT: I 384 GLU cc_start: 0.7885 (tp30) cc_final: 0.7657 (tp30) REVERT: I 386 LEU cc_start: 0.8391 (mm) cc_final: 0.8173 (mp) REVERT: I 440 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: I 459 GLU cc_start: 0.7825 (pp20) cc_final: 0.7569 (pp20) REVERT: I 460 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8332 (tp) REVERT: J 23 ARG cc_start: 0.7410 (ptt180) cc_final: 0.6941 (ptt180) REVERT: J 46 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7408 (mm) REVERT: J 58 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7274 (p) REVERT: J 60 TYR cc_start: 0.8259 (m-80) cc_final: 0.7669 (m-80) REVERT: J 97 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7960 (mmt180) REVERT: J 192 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7420 (mm110) REVERT: J 251 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7310 (mp0) REVERT: J 265 CYS cc_start: 0.8704 (m) cc_final: 0.8478 (m) REVERT: J 290 MET cc_start: 0.8872 (ttp) cc_final: 0.8592 (ttp) REVERT: J 297 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8097 (tm-30) REVERT: K 99 LYS cc_start: 0.7954 (tppp) cc_final: 0.7590 (ttmm) REVERT: K 115 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6412 (mt-10) REVERT: K 192 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7700 (mm-40) REVERT: K 193 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: K 251 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7374 (mp0) REVERT: K 289 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7887 (mtt180) REVERT: K 297 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7654 (tm-30) REVERT: K 326 LEU cc_start: 0.8491 (mp) cc_final: 0.8108 (mp) REVERT: K 417 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8247 (mp) REVERT: K 427 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: K 440 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: L 34 CYS cc_start: 0.8466 (m) cc_final: 0.8240 (m) REVERT: L 46 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (mm) REVERT: L 58 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.6956 (p) REVERT: L 60 TYR cc_start: 0.8190 (m-80) cc_final: 0.7228 (m-80) REVERT: L 192 GLN cc_start: 0.8099 (mm110) cc_final: 0.7762 (mm-40) REVERT: L 219 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7432 (mm) REVERT: L 227 SER cc_start: 0.8360 (m) cc_final: 0.7693 (t) REVERT: L 232 LEU cc_start: 0.8030 (mp) cc_final: 0.7778 (mp) REVERT: L 251 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7196 (mp0) REVERT: L 297 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7830 (tm-30) REVERT: L 364 HIS cc_start: 0.8240 (m-70) cc_final: 0.8035 (m-70) outliers start: 254 outliers final: 180 residues processed: 1078 average time/residue: 0.2408 time to fit residues: 422.3795 Evaluate side-chains 1088 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 868 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 193 GLU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 372 ASN Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 405 optimal weight: 0.8980 chunk 333 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN C 65 ASN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 432 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124462 restraints weight = 59631.960| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.72 r_work: 0.3205 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39972 Z= 0.185 Angle : 0.636 12.772 54132 Z= 0.320 Chirality : 0.046 0.227 6264 Planarity : 0.004 0.037 6972 Dihedral : 5.591 51.597 5497 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.42 % Allowed : 19.79 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 4944 helix: 0.87 (0.12), residues: 1632 sheet: -0.52 (0.14), residues: 1092 loop : -1.29 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 15 TYR 0.010 0.001 TYR C 117 PHE 0.030 0.002 PHE L 461 TRP 0.005 0.001 TRP I 122 HIS 0.009 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00435 (39948) covalent geometry : angle 0.63574 (54132) hydrogen bonds : bond 0.03604 ( 1801) hydrogen bonds : angle 4.86908 ( 4899) metal coordination : bond 0.00211 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 919 time to evaluate : 1.335 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: A 7 LYS cc_start: 0.4502 (OUTLIER) cc_final: 0.3837 (pttm) REVERT: A 55 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7374 (mmtm) REVERT: A 60 TYR cc_start: 0.8240 (m-80) cc_final: 0.7666 (m-80) REVERT: A 99 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7392 (tptp) REVERT: A 115 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6597 (tm-30) REVERT: A 192 GLN cc_start: 0.7740 (mm110) cc_final: 0.6778 (mm-40) REVERT: A 219 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7295 (mm) REVERT: A 227 SER cc_start: 0.8208 (m) cc_final: 0.7715 (t) REVERT: A 250 TYR cc_start: 0.8114 (m-80) cc_final: 0.7736 (m-80) REVERT: A 251 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7335 (mp0) REVERT: A 261 ASN cc_start: 0.6577 (t0) cc_final: 0.6338 (m-40) REVERT: A 273 ILE cc_start: 0.8407 (mt) cc_final: 0.8174 (tp) REVERT: A 289 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8167 (mtt180) REVERT: A 297 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 325 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.7082 (t-170) REVERT: A 372 ASN cc_start: 0.6410 (t0) cc_final: 0.5753 (t0) REVERT: A 417 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 440 GLU cc_start: 0.6783 (mt-10) cc_final: 0.5888 (tt0) REVERT: B 99 LYS cc_start: 0.7535 (tppp) cc_final: 0.6693 (tptp) REVERT: B 111 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: B 115 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6579 (tm-30) REVERT: B 189 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (t) REVERT: B 192 GLN cc_start: 0.7692 (mm110) cc_final: 0.7368 (mm-40) REVERT: B 219 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7048 (mm) REVERT: B 227 SER cc_start: 0.7935 (m) cc_final: 0.7454 (t) REVERT: B 234 MET cc_start: 0.7557 (mmt) cc_final: 0.6978 (mmt) REVERT: B 251 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7270 (mp0) REVERT: B 289 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7110 (mtt180) REVERT: B 297 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 326 LEU cc_start: 0.8395 (mp) cc_final: 0.8080 (mt) REVERT: B 360 ARG cc_start: 0.4785 (mtp180) cc_final: 0.3691 (mtt90) REVERT: B 371 VAL cc_start: 0.8380 (t) cc_final: 0.8155 (m) REVERT: B 372 ASN cc_start: 0.6466 (t0) cc_final: 0.5933 (t0) REVERT: B 384 GLU cc_start: 0.8079 (tp30) cc_final: 0.7879 (tp30) REVERT: B 388 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7119 (mtm180) REVERT: B 427 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7680 (t0) REVERT: B 440 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6143 (tt0) REVERT: C 192 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7282 (mm-40) REVERT: C 219 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7677 (mm) REVERT: C 227 SER cc_start: 0.8085 (m) cc_final: 0.7668 (t) REVERT: C 234 MET cc_start: 0.7443 (mmt) cc_final: 0.7120 (mmp) REVERT: C 251 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7324 (mp0) REVERT: C 261 ASN cc_start: 0.6795 (t0) cc_final: 0.6364 (m-40) REVERT: C 297 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 326 LEU cc_start: 0.8352 (mp) cc_final: 0.8026 (mt) REVERT: C 384 GLU cc_start: 0.7747 (tp30) cc_final: 0.7450 (tp30) REVERT: C 388 ARG cc_start: 0.7165 (mtm180) cc_final: 0.6687 (mtm180) REVERT: C 440 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: D 6 ARG cc_start: 0.6424 (ptp90) cc_final: 0.6093 (ptp90) REVERT: D 7 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4773 (pttm) REVERT: D 58 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7455 (p) REVERT: D 60 TYR cc_start: 0.8199 (m-80) cc_final: 0.7554 (m-80) REVERT: D 97 ARG cc_start: 0.8221 (mmt180) cc_final: 0.7857 (mmm160) REVERT: D 179 MET cc_start: 0.7349 (tpt) cc_final: 0.6989 (tpt) REVERT: D 192 GLN cc_start: 0.7916 (mm110) cc_final: 0.7292 (mm-40) REVERT: D 251 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7320 (mp0) REVERT: D 270 GLN cc_start: 0.8597 (tp40) cc_final: 0.8330 (tp40) REVERT: D 326 LEU cc_start: 0.8385 (mp) cc_final: 0.8129 (mt) REVERT: D 360 ARG cc_start: 0.4696 (mtp180) cc_final: 0.3130 (mtt-85) REVERT: E 58 SER cc_start: 0.7590 (OUTLIER) cc_final: 0.7159 (p) REVERT: E 60 TYR cc_start: 0.8222 (m-80) cc_final: 0.7950 (m-80) REVERT: E 99 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7488 (tmtt) REVERT: E 192 GLN cc_start: 0.8170 (mm110) cc_final: 0.7763 (mm-40) REVERT: E 219 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7690 (mm) REVERT: E 234 MET cc_start: 0.7303 (mtt) cc_final: 0.6853 (mmt) REVERT: E 297 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 326 LEU cc_start: 0.8293 (mp) cc_final: 0.8072 (mt) REVERT: E 372 ASN cc_start: 0.6161 (t0) cc_final: 0.5944 (t0) REVERT: E 384 GLU cc_start: 0.7917 (tp30) cc_final: 0.7687 (tp30) REVERT: E 440 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: F 60 TYR cc_start: 0.8142 (m-80) cc_final: 0.7545 (m-80) REVERT: F 139 LYS cc_start: 0.5471 (tptp) cc_final: 0.5194 (tptp) REVERT: F 219 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7333 (mm) REVERT: F 234 MET cc_start: 0.7410 (mmt) cc_final: 0.6974 (mmt) REVERT: F 251 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7355 (mp0) REVERT: F 295 ASP cc_start: 0.8955 (t0) cc_final: 0.8722 (t0) REVERT: F 297 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7930 (tm-30) REVERT: F 331 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6937 (mt-10) REVERT: F 371 VAL cc_start: 0.8538 (t) cc_final: 0.8322 (m) REVERT: F 417 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8163 (mp) REVERT: F 440 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6496 (mt-10) REVERT: G 58 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7015 (p) REVERT: G 60 TYR cc_start: 0.8327 (m-80) cc_final: 0.7729 (m-80) REVERT: G 115 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6584 (tm-30) REVERT: G 127 ASP cc_start: 0.9082 (m-30) cc_final: 0.8838 (m-30) REVERT: G 192 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7408 (mm-40) REVERT: G 193 GLU cc_start: 0.7507 (pt0) cc_final: 0.7271 (pt0) REVERT: G 219 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7262 (mm) REVERT: G 251 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7245 (mp0) REVERT: G 274 ASP cc_start: 0.8875 (m-30) cc_final: 0.8326 (m-30) REVERT: G 371 VAL cc_start: 0.8513 (t) cc_final: 0.8282 (m) REVERT: G 372 ASN cc_start: 0.6415 (t0) cc_final: 0.6157 (t0) REVERT: G 384 GLU cc_start: 0.7819 (tp30) cc_final: 0.7557 (tp30) REVERT: G 432 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: G 440 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6233 (tt0) REVERT: H 58 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.6977 (p) REVERT: H 60 TYR cc_start: 0.8228 (m-80) cc_final: 0.7495 (m-80) REVERT: H 82 ASN cc_start: 0.8559 (m-40) cc_final: 0.8131 (m-40) REVERT: H 99 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7169 (tptp) REVERT: H 189 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7491 (t) REVERT: H 227 SER cc_start: 0.8078 (m) cc_final: 0.7560 (t) REVERT: H 251 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7480 (mp0) REVERT: H 289 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7229 (mtt180) REVERT: H 297 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 326 LEU cc_start: 0.8457 (mp) cc_final: 0.8149 (mt) REVERT: H 372 ASN cc_start: 0.6076 (t0) cc_final: 0.5694 (t0) REVERT: H 427 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7689 (t0) REVERT: H 440 GLU cc_start: 0.6669 (tt0) cc_final: 0.6274 (tt0) REVERT: I 46 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7367 (mm) REVERT: I 97 ARG cc_start: 0.8156 (mmt180) cc_final: 0.7748 (mmt-90) REVERT: I 115 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6646 (tm-30) REVERT: I 139 LYS cc_start: 0.6029 (tmtt) cc_final: 0.5757 (tptp) REVERT: I 251 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7325 (mp0) REVERT: I 261 ASN cc_start: 0.6909 (t0) cc_final: 0.6538 (m-40) REVERT: I 282 LEU cc_start: 0.8708 (tp) cc_final: 0.8469 (tp) REVERT: I 289 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7585 (mtt180) REVERT: I 296 ASN cc_start: 0.8911 (m110) cc_final: 0.8654 (m-40) REVERT: I 297 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7755 (tm-30) REVERT: I 326 LEU cc_start: 0.8284 (mp) cc_final: 0.8036 (mt) REVERT: I 360 ARG cc_start: 0.4990 (mtp180) cc_final: 0.3298 (mtt90) REVERT: I 384 GLU cc_start: 0.7859 (tp30) cc_final: 0.7613 (tp30) REVERT: I 440 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6400 (tt0) REVERT: I 459 GLU cc_start: 0.7799 (pp20) cc_final: 0.7572 (pp20) REVERT: I 460 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8346 (tp) REVERT: J 21 VAL cc_start: 0.9295 (m) cc_final: 0.9091 (t) REVERT: J 23 ARG cc_start: 0.7341 (ptt180) cc_final: 0.6914 (ptt180) REVERT: J 46 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7412 (mm) REVERT: J 58 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7274 (p) REVERT: J 60 TYR cc_start: 0.8244 (m-80) cc_final: 0.7622 (m-80) REVERT: J 97 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7898 (mmt180) REVERT: J 251 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7314 (mp0) REVERT: J 265 CYS cc_start: 0.8650 (m) cc_final: 0.8442 (m) REVERT: J 289 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8246 (mtt180) REVERT: J 290 MET cc_start: 0.8876 (ttp) cc_final: 0.8605 (ttp) REVERT: J 297 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8097 (tm-30) REVERT: J 343 MET cc_start: 0.8842 (mmm) cc_final: 0.8597 (mmm) REVERT: K 99 LYS cc_start: 0.7928 (tppp) cc_final: 0.7573 (ttmm) REVERT: K 115 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6562 (mt-10) REVERT: K 192 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7743 (mm-40) REVERT: K 251 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7366 (mp0) REVERT: K 297 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7652 (tm-30) REVERT: K 326 LEU cc_start: 0.8509 (mp) cc_final: 0.8110 (mp) REVERT: K 417 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8352 (mp) REVERT: K 427 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: K 440 GLU cc_start: 0.6923 (tt0) cc_final: 0.6228 (tt0) REVERT: L 15 ARG cc_start: 0.7102 (mtt-85) cc_final: 0.6685 (mmt180) REVERT: L 34 CYS cc_start: 0.8392 (m) cc_final: 0.8174 (m) REVERT: L 46 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7315 (mm) REVERT: L 58 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7027 (p) REVERT: L 60 TYR cc_start: 0.8126 (m-80) cc_final: 0.7235 (m-80) REVERT: L 127 ASP cc_start: 0.8860 (m-30) cc_final: 0.8643 (m-30) REVERT: L 128 ARG cc_start: 0.9051 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: L 192 GLN cc_start: 0.8033 (mm110) cc_final: 0.7677 (mm-40) REVERT: L 219 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7399 (mm) REVERT: L 227 SER cc_start: 0.8531 (m) cc_final: 0.7901 (t) REVERT: L 232 LEU cc_start: 0.8070 (mp) cc_final: 0.7826 (mp) REVERT: L 251 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7184 (mp0) REVERT: L 297 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7917 (tm-30) REVERT: L 383 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8492 (p) REVERT: L 384 GLU cc_start: 0.7865 (tp30) cc_final: 0.7625 (tp30) outliers start: 232 outliers final: 169 residues processed: 1075 average time/residue: 0.2434 time to fit residues: 426.0338 Evaluate side-chains 1089 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 879 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 443 CYS Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 443 CYS Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 443 CYS Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 289 ARG Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain J residue 443 CYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain K residue 443 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 235 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 466 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 469 optimal weight: 9.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN C 29 HIS ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 308 GLN E 106 GLN E 152 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN H 296 ASN ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123948 restraints weight = 60536.816| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.91 r_work: 0.3254 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39972 Z= 0.114 Angle : 0.598 15.316 54132 Z= 0.300 Chirality : 0.044 0.180 6264 Planarity : 0.004 0.043 6972 Dihedral : 5.257 52.185 5497 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.76 % Allowed : 20.68 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 4944 helix: 1.04 (0.12), residues: 1632 sheet: -0.57 (0.14), residues: 1140 loop : -1.11 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 15 TYR 0.011 0.001 TYR C 60 PHE 0.027 0.001 PHE L 461 TRP 0.006 0.001 TRP F 122 HIS 0.006 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00254 (39948) covalent geometry : angle 0.59805 (54132) hydrogen bonds : bond 0.03151 ( 1801) hydrogen bonds : angle 4.69668 ( 4899) metal coordination : bond 0.00063 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 973 time to evaluate : 1.563 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: A 55 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7343 (mmtm) REVERT: A 60 TYR cc_start: 0.8100 (m-80) cc_final: 0.7561 (m-80) REVERT: A 99 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7216 (tptp) REVERT: A 115 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6426 (tm-30) REVERT: A 189 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7256 (t) REVERT: A 192 GLN cc_start: 0.7796 (mm110) cc_final: 0.6770 (mm110) REVERT: A 219 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7230 (mm) REVERT: A 227 SER cc_start: 0.8231 (m) cc_final: 0.7727 (t) REVERT: A 251 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7280 (mp0) REVERT: A 261 ASN cc_start: 0.6683 (t0) cc_final: 0.6440 (m-40) REVERT: A 297 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 372 ASN cc_start: 0.6267 (t0) cc_final: 0.5728 (t0) REVERT: A 417 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8221 (mp) REVERT: B 6 ARG cc_start: 0.6300 (mtm-85) cc_final: 0.5946 (ptp90) REVERT: B 46 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 115 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6519 (tm-30) REVERT: B 189 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (t) REVERT: B 192 GLN cc_start: 0.7669 (mm110) cc_final: 0.7343 (mm-40) REVERT: B 219 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6961 (mm) REVERT: B 227 SER cc_start: 0.7767 (m) cc_final: 0.7328 (t) REVERT: B 234 MET cc_start: 0.7421 (mmt) cc_final: 0.6876 (mmt) REVERT: B 251 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7182 (mp0) REVERT: B 289 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7178 (mtt180) REVERT: B 297 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 305 GLN cc_start: 0.9033 (pm20) cc_final: 0.8756 (pm20) REVERT: B 326 LEU cc_start: 0.8425 (mp) cc_final: 0.8080 (mt) REVERT: B 360 ARG cc_start: 0.4769 (mtp180) cc_final: 0.3664 (mtt90) REVERT: B 372 ASN cc_start: 0.6367 (t0) cc_final: 0.5816 (t0) REVERT: B 384 GLU cc_start: 0.8014 (tp30) cc_final: 0.7721 (tp30) REVERT: B 388 ARG cc_start: 0.7447 (mmm160) cc_final: 0.6992 (mtm180) REVERT: B 427 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 440 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6104 (tt0) REVERT: C 192 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7235 (mm-40) REVERT: C 219 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7686 (mm) REVERT: C 227 SER cc_start: 0.7991 (m) cc_final: 0.7589 (t) REVERT: C 234 MET cc_start: 0.7345 (mmt) cc_final: 0.6842 (mmt) REVERT: C 251 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7279 (mp0) REVERT: C 261 ASN cc_start: 0.6530 (t0) cc_final: 0.6278 (m-40) REVERT: C 289 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: C 297 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 326 LEU cc_start: 0.8394 (mp) cc_final: 0.8164 (mt) REVERT: C 384 GLU cc_start: 0.7680 (tp30) cc_final: 0.7381 (tp30) REVERT: C 388 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6734 (mtm180) REVERT: C 432 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: C 440 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: D 6 ARG cc_start: 0.6102 (ptp90) cc_final: 0.5546 (ptp90) REVERT: D 50 GLU cc_start: 0.7658 (tp30) cc_final: 0.7384 (mm-30) REVERT: D 58 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7628 (p) REVERT: D 60 TYR cc_start: 0.8067 (m-80) cc_final: 0.7312 (m-80) REVERT: D 92 ASP cc_start: 0.8445 (p0) cc_final: 0.8112 (p0) REVERT: D 97 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7924 (mmm160) REVERT: D 128 ARG cc_start: 0.9063 (mmt-90) cc_final: 0.8799 (mmt-90) REVERT: D 179 MET cc_start: 0.7230 (tpt) cc_final: 0.6981 (tpt) REVERT: D 192 GLN cc_start: 0.7843 (mm110) cc_final: 0.7257 (mm-40) REVERT: D 235 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7439 (mt-10) REVERT: D 253 PHE cc_start: 0.8866 (m-80) cc_final: 0.8481 (m-80) REVERT: D 270 GLN cc_start: 0.8474 (tp40) cc_final: 0.8205 (tp40) REVERT: D 326 LEU cc_start: 0.8391 (mp) cc_final: 0.8118 (mt) REVERT: D 343 MET cc_start: 0.8543 (mmm) cc_final: 0.8341 (mmm) REVERT: D 360 ARG cc_start: 0.4660 (mtp180) cc_final: 0.3120 (mtt-85) REVERT: E 58 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7434 (p) REVERT: E 60 TYR cc_start: 0.8072 (m-80) cc_final: 0.7790 (m-80) REVERT: E 99 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7302 (tmtt) REVERT: E 219 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7576 (mm) REVERT: E 261 ASN cc_start: 0.6584 (m110) cc_final: 0.5822 (m110) REVERT: E 297 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7858 (tm-30) REVERT: E 326 LEU cc_start: 0.8346 (mp) cc_final: 0.8109 (mt) REVERT: E 372 ASN cc_start: 0.5917 (t0) cc_final: 0.5683 (t0) REVERT: E 384 GLU cc_start: 0.8007 (tp30) cc_final: 0.7755 (tp30) REVERT: E 432 GLN cc_start: 0.8301 (tt0) cc_final: 0.7920 (tt0) REVERT: E 440 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: F 6 ARG cc_start: 0.5462 (mtm-85) cc_final: 0.5158 (ptt-90) REVERT: F 60 TYR cc_start: 0.7971 (m-80) cc_final: 0.7517 (m-80) REVERT: F 128 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8573 (mmt180) REVERT: F 139 LYS cc_start: 0.5499 (tptp) cc_final: 0.5233 (tptp) REVERT: F 219 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7317 (mm) REVERT: F 227 SER cc_start: 0.8030 (m) cc_final: 0.7591 (t) REVERT: F 295 ASP cc_start: 0.8892 (t0) cc_final: 0.8569 (t0) REVERT: F 297 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7888 (tm-30) REVERT: F 331 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6918 (mt-10) REVERT: F 338 MET cc_start: 0.8902 (ttt) cc_final: 0.8484 (ttt) REVERT: F 384 GLU cc_start: 0.8027 (tp30) cc_final: 0.7793 (tp30) REVERT: F 432 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: F 440 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6345 (mt-10) REVERT: G 58 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7020 (p) REVERT: G 60 TYR cc_start: 0.8217 (m-80) cc_final: 0.7610 (m-80) REVERT: G 115 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6556 (tm-30) REVERT: G 192 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7331 (mm-40) REVERT: G 193 GLU cc_start: 0.7532 (pt0) cc_final: 0.7304 (pt0) REVERT: G 219 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7067 (mm) REVERT: G 251 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7149 (mp0) REVERT: G 274 ASP cc_start: 0.8877 (m-30) cc_final: 0.8321 (m-30) REVERT: G 371 VAL cc_start: 0.8569 (t) cc_final: 0.8337 (m) REVERT: G 372 ASN cc_start: 0.6300 (t0) cc_final: 0.6023 (t0) REVERT: G 440 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6332 (tt0) REVERT: H 23 ARG cc_start: 0.7714 (ptt180) cc_final: 0.7157 (ptt180) REVERT: H 50 GLU cc_start: 0.7637 (tp30) cc_final: 0.7430 (mm-30) REVERT: H 58 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7148 (p) REVERT: H 60 TYR cc_start: 0.8119 (m-80) cc_final: 0.7427 (m-80) REVERT: H 82 ASN cc_start: 0.8510 (m-40) cc_final: 0.8129 (m-40) REVERT: H 99 LYS cc_start: 0.7871 (ttmm) cc_final: 0.6971 (tptp) REVERT: H 227 SER cc_start: 0.7949 (m) cc_final: 0.7446 (t) REVERT: H 251 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7411 (mp0) REVERT: H 289 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7727 (mtt180) REVERT: H 297 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7558 (tm-30) REVERT: H 326 LEU cc_start: 0.8471 (mp) cc_final: 0.8140 (mt) REVERT: H 372 ASN cc_start: 0.5813 (t0) cc_final: 0.5523 (t0) REVERT: H 427 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (t0) REVERT: I 115 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6503 (tm-30) REVERT: I 189 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7535 (t) REVERT: I 227 SER cc_start: 0.7894 (m) cc_final: 0.7348 (t) REVERT: I 251 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7261 (mp0) REVERT: I 261 ASN cc_start: 0.6774 (t0) cc_final: 0.6434 (m-40) REVERT: I 282 LEU cc_start: 0.8694 (tp) cc_final: 0.8487 (tp) REVERT: I 297 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7557 (tm-30) REVERT: I 326 LEU cc_start: 0.8363 (mp) cc_final: 0.8117 (mt) REVERT: I 360 ARG cc_start: 0.4956 (mtp180) cc_final: 0.3267 (mtt90) REVERT: I 384 GLU cc_start: 0.7862 (tp30) cc_final: 0.7534 (tp30) REVERT: I 460 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8387 (tp) REVERT: J 21 VAL cc_start: 0.9297 (m) cc_final: 0.9095 (t) REVERT: J 23 ARG cc_start: 0.7301 (ptt180) cc_final: 0.7044 (ptt180) REVERT: J 58 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7430 (p) REVERT: J 60 TYR cc_start: 0.8204 (m-80) cc_final: 0.7531 (m-80) REVERT: J 97 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7838 (mmt180) REVERT: J 179 MET cc_start: 0.6853 (tpt) cc_final: 0.6219 (tpt) REVERT: J 251 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7278 (mp0) REVERT: K 99 LYS cc_start: 0.7862 (tppp) cc_final: 0.7562 (ttmm) REVERT: K 115 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6355 (mt-10) REVERT: K 192 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7607 (mm110) REVERT: K 251 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7337 (mp0) REVERT: K 290 MET cc_start: 0.8701 (ttp) cc_final: 0.8431 (ttp) REVERT: K 297 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7322 (tm-30) REVERT: K 326 LEU cc_start: 0.8456 (mp) cc_final: 0.8023 (mp) REVERT: K 384 GLU cc_start: 0.7743 (tp30) cc_final: 0.7265 (tp30) REVERT: K 417 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8190 (mp) REVERT: K 440 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6296 (tt0) REVERT: L 46 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7034 (mm) REVERT: L 58 SER cc_start: 0.7648 (OUTLIER) cc_final: 0.7073 (p) REVERT: L 60 TYR cc_start: 0.7958 (m-80) cc_final: 0.7145 (m-80) REVERT: L 127 ASP cc_start: 0.8798 (m-30) cc_final: 0.8543 (m-30) REVERT: L 128 ARG cc_start: 0.8996 (mmt-90) cc_final: 0.8706 (mmt180) REVERT: L 139 LYS cc_start: 0.5472 (tptp) cc_final: 0.5241 (tptp) REVERT: L 192 GLN cc_start: 0.7936 (mm110) cc_final: 0.7577 (mm-40) REVERT: L 219 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7180 (mm) REVERT: L 227 SER cc_start: 0.8504 (m) cc_final: 0.7919 (t) REVERT: L 232 LEU cc_start: 0.8137 (mp) cc_final: 0.7915 (mp) REVERT: L 251 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7113 (mp0) REVERT: L 297 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7583 (tm-30) REVERT: L 384 GLU cc_start: 0.7782 (tp30) cc_final: 0.7429 (tp30) outliers start: 204 outliers final: 121 residues processed: 1118 average time/residue: 0.2590 time to fit residues: 470.2148 Evaluate side-chains 1053 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 898 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 443 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 443 CYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 443 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 72 optimal weight: 4.9990 chunk 327 optimal weight: 0.1980 chunk 346 optimal weight: 6.9990 chunk 396 optimal weight: 6.9990 chunk 281 optimal weight: 0.6980 chunk 271 optimal weight: 10.0000 chunk 344 optimal weight: 0.6980 chunk 365 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 144 optimal weight: 0.0270 chunk 136 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN F 11 GLN F 106 GLN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 296 ASN ** L 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125925 restraints weight = 60404.529| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.89 r_work: 0.3271 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39972 Z= 0.113 Angle : 0.610 14.223 54132 Z= 0.306 Chirality : 0.045 0.277 6264 Planarity : 0.004 0.046 6972 Dihedral : 4.989 52.299 5483 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.08 % Allowed : 21.45 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 4944 helix: 1.06 (0.12), residues: 1632 sheet: -0.77 (0.14), residues: 1248 loop : -0.99 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 15 TYR 0.013 0.001 TYR C 60 PHE 0.022 0.001 PHE L 461 TRP 0.009 0.001 TRP C 122 HIS 0.009 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00256 (39948) covalent geometry : angle 0.61050 (54132) hydrogen bonds : bond 0.03130 ( 1801) hydrogen bonds : angle 4.69337 ( 4899) metal coordination : bond 0.00076 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 969 time to evaluate : 1.557 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: A 23 ARG cc_start: 0.7566 (ptt-90) cc_final: 0.7364 (ptt180) REVERT: A 50 GLU cc_start: 0.7775 (tp30) cc_final: 0.7485 (tp30) REVERT: A 55 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7349 (mmtm) REVERT: A 60 TYR cc_start: 0.8089 (m-80) cc_final: 0.7589 (m-80) REVERT: A 99 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7247 (tptp) REVERT: A 115 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6408 (tm-30) REVERT: A 189 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7218 (t) REVERT: A 192 GLN cc_start: 0.7769 (mm110) cc_final: 0.6759 (mm110) REVERT: A 227 SER cc_start: 0.8276 (m) cc_final: 0.7793 (t) REVERT: A 251 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7387 (mp0) REVERT: A 261 ASN cc_start: 0.6686 (t0) cc_final: 0.6368 (m-40) REVERT: A 297 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 372 ASN cc_start: 0.6194 (t0) cc_final: 0.5587 (t0) REVERT: A 417 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 440 GLU cc_start: 0.6599 (mt-10) cc_final: 0.5827 (tt0) REVERT: B 46 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7023 (mm) REVERT: B 106 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7612 (mm-40) REVERT: B 115 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 192 GLN cc_start: 0.7630 (mm110) cc_final: 0.7324 (mm-40) REVERT: B 219 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6835 (mm) REVERT: B 227 SER cc_start: 0.7713 (m) cc_final: 0.7260 (t) REVERT: B 234 MET cc_start: 0.7459 (mmt) cc_final: 0.6996 (mmt) REVERT: B 289 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (mtt180) REVERT: B 297 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 305 GLN cc_start: 0.9105 (pm20) cc_final: 0.8805 (pm20) REVERT: B 326 LEU cc_start: 0.8472 (mp) cc_final: 0.8240 (mt) REVERT: B 360 ARG cc_start: 0.4770 (mtp180) cc_final: 0.3443 (mtt-85) REVERT: B 372 ASN cc_start: 0.6315 (t0) cc_final: 0.5947 (t0) REVERT: B 384 GLU cc_start: 0.7945 (tp30) cc_final: 0.7695 (tp30) REVERT: B 388 ARG cc_start: 0.7412 (mmm160) cc_final: 0.7027 (mtm180) REVERT: B 427 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 440 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6036 (tt0) REVERT: C 46 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7216 (mm) REVERT: C 50 GLU cc_start: 0.8005 (tp30) cc_final: 0.7785 (tp30) REVERT: C 55 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7465 (mmtm) REVERT: C 192 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7246 (mm110) REVERT: C 193 GLU cc_start: 0.7166 (pt0) cc_final: 0.6965 (pt0) REVERT: C 219 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7632 (mm) REVERT: C 227 SER cc_start: 0.7971 (m) cc_final: 0.7540 (t) REVERT: C 234 MET cc_start: 0.7313 (mmt) cc_final: 0.6807 (mmt) REVERT: C 251 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7293 (mp0) REVERT: C 261 ASN cc_start: 0.6752 (t0) cc_final: 0.6512 (m-40) REVERT: C 289 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8052 (mtt180) REVERT: C 297 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 326 LEU cc_start: 0.8460 (mp) cc_final: 0.8234 (mt) REVERT: C 384 GLU cc_start: 0.7708 (tp30) cc_final: 0.7376 (tp30) REVERT: C 388 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6757 (mtm180) REVERT: C 432 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: D 6 ARG cc_start: 0.5757 (ptp90) cc_final: 0.5446 (ptp90) REVERT: D 50 GLU cc_start: 0.7693 (tp30) cc_final: 0.7411 (mm-30) REVERT: D 58 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7632 (p) REVERT: D 60 TYR cc_start: 0.8040 (m-80) cc_final: 0.7175 (m-80) REVERT: D 97 ARG cc_start: 0.8202 (mmt180) cc_final: 0.7912 (mmm160) REVERT: D 179 MET cc_start: 0.7243 (tpt) cc_final: 0.6995 (tpt) REVERT: D 192 GLN cc_start: 0.7808 (mm110) cc_final: 0.7278 (mm-40) REVERT: D 227 SER cc_start: 0.7818 (m) cc_final: 0.7345 (t) REVERT: D 253 PHE cc_start: 0.8830 (m-80) cc_final: 0.8507 (m-80) REVERT: D 270 GLN cc_start: 0.8457 (tp40) cc_final: 0.8205 (tp40) REVERT: D 326 LEU cc_start: 0.8403 (mp) cc_final: 0.8111 (mt) REVERT: D 360 ARG cc_start: 0.4943 (mtp180) cc_final: 0.3275 (mtt-85) REVERT: D 372 ASN cc_start: 0.6019 (t0) cc_final: 0.5711 (t0) REVERT: E 21 VAL cc_start: 0.9277 (m) cc_final: 0.9076 (t) REVERT: E 58 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7600 (p) REVERT: E 60 TYR cc_start: 0.8130 (m-80) cc_final: 0.7840 (m-80) REVERT: E 99 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7364 (tmtt) REVERT: E 219 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7521 (mm) REVERT: E 234 MET cc_start: 0.7538 (mtt) cc_final: 0.7207 (mtt) REVERT: E 261 ASN cc_start: 0.6656 (m110) cc_final: 0.5891 (m110) REVERT: E 297 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7762 (tm-30) REVERT: E 326 LEU cc_start: 0.8300 (mp) cc_final: 0.8066 (mt) REVERT: E 372 ASN cc_start: 0.5872 (t0) cc_final: 0.5617 (t0) REVERT: E 384 GLU cc_start: 0.8045 (tp30) cc_final: 0.7775 (tp30) REVERT: E 432 GLN cc_start: 0.8298 (tt0) cc_final: 0.8064 (tt0) REVERT: E 440 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6228 (tt0) REVERT: F 50 GLU cc_start: 0.7800 (tp30) cc_final: 0.7337 (tp30) REVERT: F 60 TYR cc_start: 0.7971 (m-80) cc_final: 0.7416 (m-80) REVERT: F 106 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: F 128 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8567 (mmt180) REVERT: F 139 LYS cc_start: 0.5478 (tptp) cc_final: 0.5195 (tptp) REVERT: F 219 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7165 (mm) REVERT: F 227 SER cc_start: 0.8038 (m) cc_final: 0.7605 (t) REVERT: F 297 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7892 (tm-30) REVERT: F 331 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6906 (mt-10) REVERT: F 338 MET cc_start: 0.9010 (ttt) cc_final: 0.8629 (ttt) REVERT: F 384 GLU cc_start: 0.7892 (tp30) cc_final: 0.7615 (tp30) REVERT: F 432 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: F 440 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6249 (mt-10) REVERT: G 21 VAL cc_start: 0.9281 (m) cc_final: 0.9038 (t) REVERT: G 58 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7055 (p) REVERT: G 60 TYR cc_start: 0.8214 (m-80) cc_final: 0.7668 (m-80) REVERT: G 115 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6587 (tm-30) REVERT: G 189 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7014 (t) REVERT: G 192 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7156 (mm110) REVERT: G 193 GLU cc_start: 0.7426 (pt0) cc_final: 0.7206 (pt0) REVERT: G 219 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7036 (mm) REVERT: G 251 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7058 (mp0) REVERT: G 371 VAL cc_start: 0.8536 (t) cc_final: 0.8299 (m) REVERT: G 372 ASN cc_start: 0.6285 (t0) cc_final: 0.5995 (t0) REVERT: G 440 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: H 23 ARG cc_start: 0.7670 (ptt180) cc_final: 0.7116 (ptt180) REVERT: H 58 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7198 (p) REVERT: H 60 TYR cc_start: 0.8123 (m-80) cc_final: 0.7380 (m-80) REVERT: H 82 ASN cc_start: 0.8480 (m-40) cc_final: 0.8124 (m-40) REVERT: H 99 LYS cc_start: 0.7851 (ttmm) cc_final: 0.6958 (tptp) REVERT: H 227 SER cc_start: 0.7919 (m) cc_final: 0.7427 (t) REVERT: H 251 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7392 (mp0) REVERT: H 289 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7860 (mtt180) REVERT: H 297 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7373 (tm-30) REVERT: H 305 GLN cc_start: 0.9138 (pm20) cc_final: 0.8824 (pm20) REVERT: H 326 LEU cc_start: 0.8462 (mp) cc_final: 0.8234 (mt) REVERT: H 372 ASN cc_start: 0.5892 (t0) cc_final: 0.5537 (t0) REVERT: H 384 GLU cc_start: 0.7815 (tp30) cc_final: 0.7575 (tp30) REVERT: H 427 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7795 (t0) REVERT: I 115 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6340 (tt0) REVERT: I 227 SER cc_start: 0.7946 (m) cc_final: 0.7404 (t) REVERT: I 251 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7263 (mp0) REVERT: I 261 ASN cc_start: 0.6656 (t0) cc_final: 0.6358 (m-40) REVERT: I 297 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7524 (tm-30) REVERT: I 326 LEU cc_start: 0.8359 (mp) cc_final: 0.8096 (mt) REVERT: I 360 ARG cc_start: 0.4830 (mtp180) cc_final: 0.3266 (mtt90) REVERT: I 384 GLU cc_start: 0.7835 (tp30) cc_final: 0.7499 (tp30) REVERT: I 440 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: I 460 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8357 (tp) REVERT: J 23 ARG cc_start: 0.7331 (ptt180) cc_final: 0.6991 (ptt180) REVERT: J 44 HIS cc_start: 0.6234 (p-80) cc_final: 0.6014 (t70) REVERT: J 46 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7206 (mm) REVERT: J 58 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7444 (p) REVERT: J 60 TYR cc_start: 0.8192 (m-80) cc_final: 0.7413 (m-80) REVERT: J 97 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7875 (mmt180) REVERT: J 179 MET cc_start: 0.6817 (tpt) cc_final: 0.6195 (tpt) REVERT: J 251 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7268 (mp0) REVERT: J 289 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8219 (mtt180) REVERT: J 338 MET cc_start: 0.9155 (ttt) cc_final: 0.8915 (ttm) REVERT: J 398 LEU cc_start: 0.9006 (mp) cc_final: 0.8778 (mp) REVERT: K 99 LYS cc_start: 0.7828 (tppp) cc_final: 0.7524 (ttmm) REVERT: K 115 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6373 (mt-10) REVERT: K 192 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7587 (mm-40) REVERT: K 251 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7390 (mp0) REVERT: K 289 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7886 (mtt180) REVERT: K 290 MET cc_start: 0.8696 (ttp) cc_final: 0.8483 (ttp) REVERT: K 297 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7547 (tm-30) REVERT: K 326 LEU cc_start: 0.8389 (mp) cc_final: 0.7959 (mp) REVERT: K 402 MET cc_start: 0.4717 (pmm) cc_final: 0.4085 (mmt) REVERT: K 417 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8133 (mp) REVERT: K 432 GLN cc_start: 0.8677 (tt0) cc_final: 0.8105 (tt0) REVERT: K 440 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6148 (tt0) REVERT: L 19 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8276 (mtmt) REVERT: L 46 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6991 (mm) REVERT: L 58 SER cc_start: 0.7694 (OUTLIER) cc_final: 0.7103 (p) REVERT: L 60 TYR cc_start: 0.7948 (m-80) cc_final: 0.7130 (m-80) REVERT: L 115 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6248 (tm-30) REVERT: L 127 ASP cc_start: 0.8804 (m-30) cc_final: 0.8555 (m-30) REVERT: L 128 ARG cc_start: 0.8990 (mmt-90) cc_final: 0.8686 (mmt180) REVERT: L 139 LYS cc_start: 0.5337 (tptp) cc_final: 0.5081 (tptp) REVERT: L 192 GLN cc_start: 0.7899 (mm110) cc_final: 0.7525 (mm-40) REVERT: L 219 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6989 (mm) REVERT: L 227 SER cc_start: 0.8537 (m) cc_final: 0.7982 (t) REVERT: L 251 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7098 (mp0) REVERT: L 274 ASP cc_start: 0.8873 (m-30) cc_final: 0.8506 (m-30) REVERT: L 297 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7612 (tm-30) REVERT: L 384 GLU cc_start: 0.7724 (tp30) cc_final: 0.7360 (tp30) outliers start: 175 outliers final: 114 residues processed: 1094 average time/residue: 0.2513 time to fit residues: 448.0512 Evaluate side-chains 1059 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 908 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 289 ARG Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 309 SER Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 4 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 354 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN F 192 GLN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 65 ASN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN L 111 GLN ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN L 380 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127234 restraints weight = 59797.931| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.77 r_work: 0.3252 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39972 Z= 0.153 Angle : 0.657 13.978 54132 Z= 0.327 Chirality : 0.046 0.217 6264 Planarity : 0.005 0.056 6972 Dihedral : 5.091 52.247 5480 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.11 % Allowed : 22.13 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.51 (0.11), residues: 4944 helix: 0.98 (0.12), residues: 1632 sheet: -0.79 (0.14), residues: 1248 loop : -1.02 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 15 TYR 0.015 0.001 TYR C 60 PHE 0.025 0.002 PHE L 461 TRP 0.008 0.001 TRP H 122 HIS 0.006 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00358 (39948) covalent geometry : angle 0.65653 (54132) hydrogen bonds : bond 0.03328 ( 1801) hydrogen bonds : angle 4.79250 ( 4899) metal coordination : bond 0.00154 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 910 time to evaluate : 1.590 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: A 50 GLU cc_start: 0.7794 (tp30) cc_final: 0.7499 (tp30) REVERT: A 55 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7393 (mmtm) REVERT: A 60 TYR cc_start: 0.8158 (m-80) cc_final: 0.7607 (m-80) REVERT: A 99 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7294 (tptp) REVERT: A 115 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6513 (tm-30) REVERT: A 192 GLN cc_start: 0.7819 (mm110) cc_final: 0.7569 (mm110) REVERT: A 227 SER cc_start: 0.8281 (m) cc_final: 0.7801 (t) REVERT: A 251 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7376 (mp0) REVERT: A 297 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 372 ASN cc_start: 0.6074 (t0) cc_final: 0.5561 (t0) REVERT: A 417 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 440 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5877 (tt0) REVERT: B 115 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6592 (tm-30) REVERT: B 192 GLN cc_start: 0.7748 (mm110) cc_final: 0.7476 (mm-40) REVERT: B 219 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6890 (mm) REVERT: B 227 SER cc_start: 0.7806 (m) cc_final: 0.7366 (t) REVERT: B 234 MET cc_start: 0.7488 (mmt) cc_final: 0.6939 (mmt) REVERT: B 289 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8140 (mtt180) REVERT: B 297 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 305 GLN cc_start: 0.9107 (pm20) cc_final: 0.8802 (pm20) REVERT: B 326 LEU cc_start: 0.8467 (mp) cc_final: 0.8248 (mt) REVERT: B 360 ARG cc_start: 0.4838 (mtp180) cc_final: 0.3616 (mtt90) REVERT: B 384 GLU cc_start: 0.7953 (tp30) cc_final: 0.7713 (tp30) REVERT: B 388 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7054 (mtm180) REVERT: B 427 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 440 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6187 (tt0) REVERT: C 46 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7251 (mm) REVERT: C 193 GLU cc_start: 0.7307 (pt0) cc_final: 0.7095 (pt0) REVERT: C 219 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 227 SER cc_start: 0.8071 (m) cc_final: 0.7661 (t) REVERT: C 234 MET cc_start: 0.7269 (mmt) cc_final: 0.6630 (mmt) REVERT: C 251 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7304 (mp0) REVERT: C 261 ASN cc_start: 0.6782 (t0) cc_final: 0.6410 (m-40) REVERT: C 289 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8118 (mtt180) REVERT: C 297 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7717 (tm-30) REVERT: C 326 LEU cc_start: 0.8348 (mp) cc_final: 0.8120 (mt) REVERT: C 384 GLU cc_start: 0.7772 (tp30) cc_final: 0.7407 (tp30) REVERT: C 388 ARG cc_start: 0.7026 (mtm180) cc_final: 0.6604 (mtm180) REVERT: C 432 GLN cc_start: 0.8705 (tt0) cc_final: 0.8450 (tt0) REVERT: C 440 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6076 (tt0) REVERT: D 58 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7642 (p) REVERT: D 60 TYR cc_start: 0.8081 (m-80) cc_final: 0.7306 (m-80) REVERT: D 97 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7956 (mmm160) REVERT: D 179 MET cc_start: 0.7266 (tpt) cc_final: 0.7006 (tpt) REVERT: D 192 GLN cc_start: 0.7822 (mm110) cc_final: 0.7345 (mm-40) REVERT: D 227 SER cc_start: 0.7892 (m) cc_final: 0.7435 (t) REVERT: D 235 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7544 (mt-10) REVERT: D 253 PHE cc_start: 0.8852 (m-80) cc_final: 0.8544 (m-80) REVERT: D 326 LEU cc_start: 0.8379 (mp) cc_final: 0.8108 (mt) REVERT: D 360 ARG cc_start: 0.4908 (mtp180) cc_final: 0.3248 (mtt-85) REVERT: D 372 ASN cc_start: 0.6217 (t0) cc_final: 0.5876 (t0) REVERT: E 58 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7586 (p) REVERT: E 60 TYR cc_start: 0.8136 (m-80) cc_final: 0.7853 (m-80) REVERT: E 99 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7426 (tmtt) REVERT: E 219 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7611 (mm) REVERT: E 234 MET cc_start: 0.7418 (mtt) cc_final: 0.7176 (mtt) REVERT: E 235 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7745 (mt-10) REVERT: E 261 ASN cc_start: 0.6668 (m110) cc_final: 0.5897 (m110) REVERT: E 297 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7812 (tm-30) REVERT: E 326 LEU cc_start: 0.8305 (mp) cc_final: 0.8078 (mt) REVERT: E 372 ASN cc_start: 0.5952 (t0) cc_final: 0.5714 (t0) REVERT: E 384 GLU cc_start: 0.8070 (tp30) cc_final: 0.7771 (tp30) REVERT: E 432 GLN cc_start: 0.8396 (tt0) cc_final: 0.8086 (tt0) REVERT: E 440 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: F 50 GLU cc_start: 0.7881 (tp30) cc_final: 0.7433 (tp30) REVERT: F 60 TYR cc_start: 0.8019 (m-80) cc_final: 0.7482 (m-80) REVERT: F 106 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: F 128 ARG cc_start: 0.9001 (mmt-90) cc_final: 0.8588 (mmt180) REVERT: F 139 LYS cc_start: 0.5562 (tptp) cc_final: 0.5284 (tptp) REVERT: F 219 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7210 (mm) REVERT: F 227 SER cc_start: 0.8108 (m) cc_final: 0.7665 (t) REVERT: F 274 ASP cc_start: 0.8838 (m-30) cc_final: 0.8395 (m-30) REVERT: F 297 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7896 (tm-30) REVERT: F 331 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6909 (mt-10) REVERT: F 384 GLU cc_start: 0.7920 (tp30) cc_final: 0.7631 (tp30) REVERT: F 432 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: F 440 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6319 (mt-10) REVERT: G 24 SER cc_start: 0.9197 (m) cc_final: 0.8966 (m) REVERT: G 58 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7119 (p) REVERT: G 60 TYR cc_start: 0.8255 (m-80) cc_final: 0.7728 (m-80) REVERT: G 115 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6661 (tm-30) REVERT: G 192 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7368 (mm110) REVERT: G 193 GLU cc_start: 0.7335 (pt0) cc_final: 0.7117 (pt0) REVERT: G 251 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7118 (mp0) REVERT: G 289 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8215 (mtt180) REVERT: G 371 VAL cc_start: 0.8474 (t) cc_final: 0.8218 (m) REVERT: G 372 ASN cc_start: 0.6294 (t0) cc_final: 0.5989 (t0) REVERT: G 440 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6124 (tt0) REVERT: H 23 ARG cc_start: 0.7683 (ptt180) cc_final: 0.7070 (ptt180) REVERT: H 58 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7103 (p) REVERT: H 60 TYR cc_start: 0.8097 (m-80) cc_final: 0.7356 (m-80) REVERT: H 82 ASN cc_start: 0.8560 (m-40) cc_final: 0.8199 (m-40) REVERT: H 99 LYS cc_start: 0.7953 (ttmm) cc_final: 0.6996 (tptp) REVERT: H 227 SER cc_start: 0.7996 (m) cc_final: 0.7501 (t) REVERT: H 251 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7411 (mp0) REVERT: H 289 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7869 (mtt180) REVERT: H 297 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7506 (tm-30) REVERT: H 305 GLN cc_start: 0.9106 (pm20) cc_final: 0.8900 (pm20) REVERT: H 326 LEU cc_start: 0.8462 (mp) cc_final: 0.8231 (mt) REVERT: H 372 ASN cc_start: 0.5823 (t0) cc_final: 0.5501 (t0) REVERT: H 427 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7749 (t0) REVERT: I 115 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6511 (tm-30) REVERT: I 227 SER cc_start: 0.8013 (m) cc_final: 0.7427 (t) REVERT: I 235 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7139 (mt-10) REVERT: I 251 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7311 (mp0) REVERT: I 261 ASN cc_start: 0.6718 (t0) cc_final: 0.6443 (m-40) REVERT: I 297 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7602 (tm-30) REVERT: I 326 LEU cc_start: 0.8309 (mp) cc_final: 0.8047 (mt) REVERT: I 384 GLU cc_start: 0.7839 (tp30) cc_final: 0.7502 (tp30) REVERT: I 440 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6142 (tt0) REVERT: J 23 ARG cc_start: 0.7334 (ptt180) cc_final: 0.7091 (ptt180) REVERT: J 46 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7229 (mm) REVERT: J 58 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7405 (p) REVERT: J 60 TYR cc_start: 0.8198 (m-80) cc_final: 0.7467 (m-80) REVERT: J 97 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7879 (mmt180) REVERT: J 179 MET cc_start: 0.6858 (tpt) cc_final: 0.6246 (tpt) REVERT: J 251 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7364 (mp0) REVERT: K 23 ARG cc_start: 0.7563 (ptt180) cc_final: 0.6799 (ptt180) REVERT: K 99 LYS cc_start: 0.7860 (tppp) cc_final: 0.7563 (ttmm) REVERT: K 115 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6421 (mt-10) REVERT: K 192 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7624 (mm-40) REVERT: K 251 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7464 (mp0) REVERT: K 289 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7942 (mtt180) REVERT: K 290 MET cc_start: 0.8733 (ttp) cc_final: 0.8448 (ttp) REVERT: K 297 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7640 (tm-30) REVERT: K 326 LEU cc_start: 0.8382 (mp) cc_final: 0.7960 (mp) REVERT: K 402 MET cc_start: 0.4396 (pmm) cc_final: 0.3905 (mmt) REVERT: K 417 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8228 (mp) REVERT: K 432 GLN cc_start: 0.8689 (tt0) cc_final: 0.8093 (tt0) REVERT: K 440 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6177 (tt0) REVERT: L 46 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7009 (mm) REVERT: L 58 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7041 (p) REVERT: L 60 TYR cc_start: 0.8011 (m-80) cc_final: 0.7280 (m-80) REVERT: L 115 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6351 (tm-30) REVERT: L 127 ASP cc_start: 0.8854 (m-30) cc_final: 0.8609 (m-30) REVERT: L 128 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8687 (mmt180) REVERT: L 139 LYS cc_start: 0.5390 (tptp) cc_final: 0.5135 (tptp) REVERT: L 219 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7068 (mm) REVERT: L 227 SER cc_start: 0.8561 (m) cc_final: 0.8010 (t) REVERT: L 251 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7187 (mp0) REVERT: L 274 ASP cc_start: 0.8853 (m-30) cc_final: 0.8499 (m-30) REVERT: L 297 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7549 (tm-30) REVERT: L 384 GLU cc_start: 0.7726 (tp30) cc_final: 0.7370 (tp30) outliers start: 176 outliers final: 122 residues processed: 1035 average time/residue: 0.2506 time to fit residues: 425.5898 Evaluate side-chains 1038 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 884 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 443 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 325 HIS Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 383 SER Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 296 ASN Chi-restraints excluded: chain I residue 345 HIS Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 413 ILE Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 440 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 400 ASP Chi-restraints excluded: chain J residue 427 ASP Chi-restraints excluded: chain J residue 441 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 345 HIS Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 426 LEU Chi-restraints excluded: chain K residue 440 GLU Chi-restraints excluded: chain K residue 441 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 345 HIS Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 330 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 387 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 442 optimal weight: 0.9990 chunk 189 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 chunk 356 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN C 40 GLN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN E 296 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** L 380 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 = 0.3619 r_free = 0.3619 target = 0.144859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124117 restraints weight = 60972.468| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.85 r_work: 0.3250 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 39972 Z= 0.235 Angle : 1.061 59.168 54132 Z= 0.637 Chirality : 0.047 0.431 6264 Planarity : 0.006 0.207 6972 Dihedral : 5.078 50.586 5478 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 4.32 % Allowed : 21.85 % Favored : 73.83 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4944 helix: 0.98 (0.12), residues: 1632 sheet: -0.80 (0.14), residues: 1248 loop : -1.05 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 97 TYR 0.013 0.001 TYR C 60 PHE 0.022 0.002 PHE L 461 TRP 0.007 0.001 TRP H 122 HIS 0.019 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00487 (39948) covalent geometry : angle 1.06095 (54132) hydrogen bonds : bond 0.03368 ( 1801) hydrogen bonds : angle 4.79930 ( 4899) metal coordination : bond 0.00175 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9741.87 seconds wall clock time: 168 minutes 33.09 seconds (10113.09 seconds total)