Starting phenix.real_space_refine on Sat Sep 28 19:28:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwx_10045/09_2024/6rwx_10045.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 45024 2.51 5 N 12048 2.21 5 O 13728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 240 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70968 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1554 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain: "a" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X, c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, s, r, u, t, w, v, x Time building chain proxies: 11.67, per 1000 atoms: 0.16 Number of scatterers: 70968 At special positions: 0 Unit cell: (255.983, 255.983, 78.8703, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 13728 8.00 N 12048 7.00 C 45024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 170 " - pdb=" SG CYS S 196 " distance=2.03 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: 12.58 Conformation dependent library (CDL) restraints added in 6.8 seconds 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16992 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 120 sheets defined 43.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'S' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE S 157 " --> pdb=" O ILE S 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP S 158 " --> pdb=" O ALA S 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 153 through 158' Processing helix chain 'S' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR S 191 " --> pdb=" O ALA S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 217 Processing helix chain 'S' and resid 246 through 261 Processing helix chain 'S' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA S 277 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 310 through 329 Processing helix chain 'T' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE T 157 " --> pdb=" O ILE T 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP T 158 " --> pdb=" O ALA T 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 153 through 158' Processing helix chain 'T' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR T 191 " --> pdb=" O ALA T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 217 Processing helix chain 'T' and resid 246 through 261 Processing helix chain 'T' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA T 277 " --> pdb=" O SER T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 310 through 329 Processing helix chain 'R' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 153 through 158' Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR R 191 " --> pdb=" O ALA R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 217 Processing helix chain 'R' and resid 246 through 261 Processing helix chain 'R' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 329 Processing helix chain 'Q' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE Q 157 " --> pdb=" O ILE Q 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP Q 158 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 153 through 158' Processing helix chain 'Q' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 201 through 217 Processing helix chain 'Q' and resid 246 through 261 Processing helix chain 'Q' and resid 273 through 288 removed outlier: 3.545A pdb=" N ALA Q 277 " --> pdb=" O SER Q 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 329 Processing helix chain 'P' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE P 157 " --> pdb=" O ILE P 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP P 158 " --> pdb=" O ALA P 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 153 through 158' Processing helix chain 'P' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR P 191 " --> pdb=" O ALA P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 217 Processing helix chain 'P' and resid 246 through 261 Processing helix chain 'P' and resid 273 through 288 removed outlier: 3.547A pdb=" N ALA P 277 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 329 Processing helix chain 'O' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE O 157 " --> pdb=" O ILE O 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 153 through 158' Processing helix chain 'O' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR O 191 " --> pdb=" O ALA O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 217 Processing helix chain 'O' and resid 246 through 261 Processing helix chain 'O' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA O 277 " --> pdb=" O SER O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 329 Processing helix chain 'N' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE N 157 " --> pdb=" O ILE N 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP N 158 " --> pdb=" O ALA N 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 153 through 158' Processing helix chain 'N' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 246 through 261 Processing helix chain 'N' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA N 277 " --> pdb=" O SER N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 329 Processing helix chain 'M' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE M 157 " --> pdb=" O ILE M 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 153 through 158' Processing helix chain 'M' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR M 191 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 217 Processing helix chain 'M' and resid 246 through 261 Processing helix chain 'M' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 329 Processing helix chain 'L' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE L 157 " --> pdb=" O ILE L 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 153 through 158' Processing helix chain 'L' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 217 Processing helix chain 'L' and resid 246 through 261 Processing helix chain 'L' and resid 273 through 288 removed outlier: 3.547A pdb=" N ALA L 277 " --> pdb=" O SER L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 329 Processing helix chain 'K' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 153 through 158' Processing helix chain 'K' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 217 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA K 277 " --> pdb=" O SER K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 329 Processing helix chain 'J' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 153 through 158' Processing helix chain 'J' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 217 Processing helix chain 'J' and resid 246 through 261 Processing helix chain 'J' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA J 277 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 329 Processing helix chain 'I' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE I 157 " --> pdb=" O ILE I 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 153 through 158' Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.741A pdb=" N THR I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 217 Processing helix chain 'I' and resid 246 through 261 Processing helix chain 'I' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 329 Processing helix chain 'H' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE H 157 " --> pdb=" O ILE H 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 153 through 158' Processing helix chain 'H' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 217 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 273 through 288 removed outlier: 3.547A pdb=" N ALA H 277 " --> pdb=" O SER H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 329 Processing helix chain 'G' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 153 through 158' Processing helix chain 'G' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR G 191 " --> pdb=" O ALA G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 217 Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 329 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE F 157 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 153 through 158' Processing helix chain 'F' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 217 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 329 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 217 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 273 through 288 removed outlier: 3.545A pdb=" N ALA E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 329 Processing helix chain 'D' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 153 through 158' Processing helix chain 'D' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 217 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'C' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 158' Processing helix chain 'C' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 217 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 329 Processing helix chain 'B' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 158' Processing helix chain 'B' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'A' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 158' Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'W' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE W 157 " --> pdb=" O ILE W 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP W 158 " --> pdb=" O ALA W 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 153 through 158' Processing helix chain 'W' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 201 through 217 Processing helix chain 'W' and resid 246 through 261 Processing helix chain 'W' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA W 277 " --> pdb=" O SER W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 329 Processing helix chain 'V' and resid 153 through 158 removed outlier: 4.092A pdb=" N ILE V 157 " --> pdb=" O ILE V 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP V 158 " --> pdb=" O ALA V 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 153 through 158' Processing helix chain 'V' and resid 177 through 191 removed outlier: 3.742A pdb=" N THR V 191 " --> pdb=" O ALA V 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 201 through 217 Processing helix chain 'V' and resid 246 through 261 Processing helix chain 'V' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA V 277 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing helix chain 'V' and resid 310 through 329 Processing helix chain 'U' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE U 157 " --> pdb=" O ILE U 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 153 through 158' Processing helix chain 'U' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR U 191 " --> pdb=" O ALA U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 217 Processing helix chain 'U' and resid 246 through 261 Processing helix chain 'U' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA U 277 " --> pdb=" O SER U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 310 through 329 Processing helix chain 'X' and resid 153 through 158 removed outlier: 4.091A pdb=" N ILE X 157 " --> pdb=" O ILE X 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP X 158 " --> pdb=" O ALA X 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 153 through 158' Processing helix chain 'X' and resid 177 through 191 removed outlier: 3.743A pdb=" N THR X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 201 through 217 Processing helix chain 'X' and resid 246 through 261 Processing helix chain 'X' and resid 273 through 288 removed outlier: 3.546A pdb=" N ALA X 277 " --> pdb=" O SER X 273 " (cutoff:3.500A) Processing helix chain 'X' and resid 310 through 329 Processing helix chain 'a' and resid 29 through 43 Processing helix chain 'a' and resid 65 through 77 Processing helix chain 'a' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE a 90 " --> pdb=" O SER a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 98 through 118 Processing helix chain 'a' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN a 172 " --> pdb=" O ARG a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 180 No H-bonds generated for 'chain 'a' and resid 178 through 180' Processing helix chain 'b' and resid 29 through 43 Processing helix chain 'b' and resid 65 through 77 Processing helix chain 'b' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE b 90 " --> pdb=" O SER b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 118 Processing helix chain 'b' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN b 172 " --> pdb=" O ARG b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 178 through 180 No H-bonds generated for 'chain 'b' and resid 178 through 180' Processing helix chain 'c' and resid 29 through 43 Processing helix chain 'c' and resid 65 through 77 Processing helix chain 'c' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE c 90 " --> pdb=" O SER c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 118 Processing helix chain 'c' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN c 172 " --> pdb=" O ARG c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 180 No H-bonds generated for 'chain 'c' and resid 178 through 180' Processing helix chain 'd' and resid 29 through 43 Processing helix chain 'd' and resid 65 through 77 Processing helix chain 'd' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE d 90 " --> pdb=" O SER d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 118 Processing helix chain 'd' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN d 172 " --> pdb=" O ARG d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 180 No H-bonds generated for 'chain 'd' and resid 178 through 180' Processing helix chain 'e' and resid 29 through 43 Processing helix chain 'e' and resid 65 through 77 Processing helix chain 'e' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE e 90 " --> pdb=" O SER e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 118 Processing helix chain 'e' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN e 172 " --> pdb=" O ARG e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 178 through 180 No H-bonds generated for 'chain 'e' and resid 178 through 180' Processing helix chain 'f' and resid 29 through 43 Processing helix chain 'f' and resid 65 through 77 Processing helix chain 'f' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE f 90 " --> pdb=" O SER f 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 118 Processing helix chain 'f' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN f 172 " --> pdb=" O ARG f 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 178 through 180 No H-bonds generated for 'chain 'f' and resid 178 through 180' Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 65 through 77 Processing helix chain 'g' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE g 90 " --> pdb=" O SER g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 98 through 118 Processing helix chain 'g' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN g 172 " --> pdb=" O ARG g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 178 through 180 No H-bonds generated for 'chain 'g' and resid 178 through 180' Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 65 through 77 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE h 90 " --> pdb=" O SER h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 118 Processing helix chain 'h' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN h 172 " --> pdb=" O ARG h 168 " (cutoff:3.500A) Processing helix chain 'h' and resid 178 through 180 No H-bonds generated for 'chain 'h' and resid 178 through 180' Processing helix chain 'i' and resid 29 through 43 Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE i 90 " --> pdb=" O SER i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 118 Processing helix chain 'i' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN i 172 " --> pdb=" O ARG i 168 " (cutoff:3.500A) Processing helix chain 'i' and resid 178 through 180 No H-bonds generated for 'chain 'i' and resid 178 through 180' Processing helix chain 'j' and resid 29 through 43 Processing helix chain 'j' and resid 65 through 77 Processing helix chain 'j' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE j 90 " --> pdb=" O SER j 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 118 Processing helix chain 'j' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN j 172 " --> pdb=" O ARG j 168 " (cutoff:3.500A) Processing helix chain 'j' and resid 178 through 180 No H-bonds generated for 'chain 'j' and resid 178 through 180' Processing helix chain 'k' and resid 29 through 43 Processing helix chain 'k' and resid 65 through 77 Processing helix chain 'k' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE k 90 " --> pdb=" O SER k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 98 through 118 Processing helix chain 'k' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN k 172 " --> pdb=" O ARG k 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 178 through 180 No H-bonds generated for 'chain 'k' and resid 178 through 180' Processing helix chain 'l' and resid 29 through 43 Processing helix chain 'l' and resid 65 through 77 Processing helix chain 'l' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE l 90 " --> pdb=" O SER l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 98 through 118 Processing helix chain 'l' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN l 172 " --> pdb=" O ARG l 168 " (cutoff:3.500A) Processing helix chain 'l' and resid 178 through 180 No H-bonds generated for 'chain 'l' and resid 178 through 180' Processing helix chain 'm' and resid 29 through 43 Processing helix chain 'm' and resid 65 through 77 Processing helix chain 'm' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE m 90 " --> pdb=" O SER m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 98 through 118 Processing helix chain 'm' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN m 172 " --> pdb=" O ARG m 168 " (cutoff:3.500A) Processing helix chain 'm' and resid 178 through 180 No H-bonds generated for 'chain 'm' and resid 178 through 180' Processing helix chain 'n' and resid 29 through 43 Processing helix chain 'n' and resid 65 through 77 Processing helix chain 'n' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE n 90 " --> pdb=" O SER n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 118 Processing helix chain 'n' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN n 172 " --> pdb=" O ARG n 168 " (cutoff:3.500A) Processing helix chain 'n' and resid 178 through 180 No H-bonds generated for 'chain 'n' and resid 178 through 180' Processing helix chain 'o' and resid 29 through 43 Processing helix chain 'o' and resid 65 through 77 Processing helix chain 'o' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE o 90 " --> pdb=" O SER o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 98 through 118 Processing helix chain 'o' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN o 172 " --> pdb=" O ARG o 168 " (cutoff:3.500A) Processing helix chain 'o' and resid 178 through 180 No H-bonds generated for 'chain 'o' and resid 178 through 180' Processing helix chain 'p' and resid 29 through 43 Processing helix chain 'p' and resid 65 through 77 Processing helix chain 'p' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE p 90 " --> pdb=" O SER p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 98 through 118 Processing helix chain 'p' and resid 161 through 172 removed outlier: 4.270A pdb=" N ASN p 172 " --> pdb=" O ARG p 168 " (cutoff:3.500A) Processing helix chain 'p' and resid 178 through 180 No H-bonds generated for 'chain 'p' and resid 178 through 180' Processing helix chain 'q' and resid 29 through 43 Processing helix chain 'q' and resid 65 through 77 Processing helix chain 'q' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE q 90 " --> pdb=" O SER q 87 " (cutoff:3.500A) Processing helix chain 'q' and resid 98 through 118 Processing helix chain 'q' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN q 172 " --> pdb=" O ARG q 168 " (cutoff:3.500A) Processing helix chain 'q' and resid 178 through 180 No H-bonds generated for 'chain 'q' and resid 178 through 180' Processing helix chain 'r' and resid 29 through 43 Processing helix chain 'r' and resid 65 through 77 Processing helix chain 'r' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE r 90 " --> pdb=" O SER r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 98 through 118 Processing helix chain 'r' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN r 172 " --> pdb=" O ARG r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 180 No H-bonds generated for 'chain 'r' and resid 178 through 180' Processing helix chain 's' and resid 29 through 43 Processing helix chain 's' and resid 65 through 77 Processing helix chain 's' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE s 90 " --> pdb=" O SER s 87 " (cutoff:3.500A) Processing helix chain 's' and resid 98 through 118 Processing helix chain 's' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN s 172 " --> pdb=" O ARG s 168 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 180 No H-bonds generated for 'chain 's' and resid 178 through 180' Processing helix chain 't' and resid 29 through 43 Processing helix chain 't' and resid 65 through 77 Processing helix chain 't' and resid 85 through 90 removed outlier: 3.529A pdb=" N PHE t 90 " --> pdb=" O SER t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 98 through 118 Processing helix chain 't' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN t 172 " --> pdb=" O ARG t 168 " (cutoff:3.500A) Processing helix chain 't' and resid 178 through 180 No H-bonds generated for 'chain 't' and resid 178 through 180' Processing helix chain 'u' and resid 29 through 43 Processing helix chain 'u' and resid 65 through 77 Processing helix chain 'u' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE u 90 " --> pdb=" O SER u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 98 through 118 Processing helix chain 'u' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN u 172 " --> pdb=" O ARG u 168 " (cutoff:3.500A) Processing helix chain 'u' and resid 178 through 180 No H-bonds generated for 'chain 'u' and resid 178 through 180' Processing helix chain 'v' and resid 29 through 43 Processing helix chain 'v' and resid 65 through 77 Processing helix chain 'v' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE v 90 " --> pdb=" O SER v 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 98 through 118 Processing helix chain 'v' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN v 172 " --> pdb=" O ARG v 168 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 180 No H-bonds generated for 'chain 'v' and resid 178 through 180' Processing helix chain 'w' and resid 29 through 43 Processing helix chain 'w' and resid 65 through 77 Processing helix chain 'w' and resid 85 through 90 removed outlier: 3.530A pdb=" N PHE w 90 " --> pdb=" O SER w 87 " (cutoff:3.500A) Processing helix chain 'w' and resid 98 through 118 Processing helix chain 'w' and resid 161 through 172 removed outlier: 4.269A pdb=" N ASN w 172 " --> pdb=" O ARG w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 178 through 180 No H-bonds generated for 'chain 'w' and resid 178 through 180' Processing helix chain 'x' and resid 29 through 43 Processing helix chain 'x' and resid 65 through 77 Processing helix chain 'x' and resid 85 through 90 removed outlier: 3.531A pdb=" N PHE x 90 " --> pdb=" O SER x 87 " (cutoff:3.500A) Processing helix chain 'x' and resid 98 through 118 Processing helix chain 'x' and resid 161 through 172 removed outlier: 4.268A pdb=" N ASN x 172 " --> pdb=" O ARG x 168 " (cutoff:3.500A) Processing helix chain 'x' and resid 178 through 180 No H-bonds generated for 'chain 'x' and resid 178 through 180' Processing sheet with id=AA1, first strand: chain 'S' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN S 171 " --> pdb=" O TYR S 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU S 200 " --> pdb=" O ASN S 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE S 173 " --> pdb=" O LEU S 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU S 234 " --> pdb=" O LYS S 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN S 270 " --> pdb=" O LEU S 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL S 236 " --> pdb=" O ASN S 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU S 272 " --> pdb=" O VAL S 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU S 238 " --> pdb=" O LEU S 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL S 301 " --> pdb=" O GLU S 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER S 336 " --> pdb=" O VAL S 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR S 303 " --> pdb=" O SER S 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 163 through 166 removed outlier: 6.487A pdb=" N ASN T 171 " --> pdb=" O TYR T 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU T 200 " --> pdb=" O ASN T 171 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE T 173 " --> pdb=" O LEU T 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU T 234 " --> pdb=" O LYS T 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN T 270 " --> pdb=" O LEU T 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL T 236 " --> pdb=" O ASN T 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU T 272 " --> pdb=" O VAL T 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU T 238 " --> pdb=" O LEU T 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL T 301 " --> pdb=" O GLU T 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER T 336 " --> pdb=" O VAL T 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR T 303 " --> pdb=" O SER T 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN R 171 " --> pdb=" O TYR R 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU R 200 " --> pdb=" O ASN R 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE R 173 " --> pdb=" O LEU R 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU R 234 " --> pdb=" O LYS R 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN R 270 " --> pdb=" O LEU R 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL R 236 " --> pdb=" O ASN R 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU R 272 " --> pdb=" O VAL R 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU R 238 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL R 301 " --> pdb=" O GLU R 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER R 336 " --> pdb=" O VAL R 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR R 303 " --> pdb=" O SER R 336 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN Q 171 " --> pdb=" O TYR Q 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU Q 200 " --> pdb=" O ASN Q 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE Q 173 " --> pdb=" O LEU Q 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU Q 234 " --> pdb=" O LYS Q 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN Q 270 " --> pdb=" O LEU Q 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL Q 236 " --> pdb=" O ASN Q 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU Q 272 " --> pdb=" O VAL Q 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU Q 238 " --> pdb=" O LEU Q 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL Q 301 " --> pdb=" O GLU Q 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER Q 336 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR Q 303 " --> pdb=" O SER Q 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN P 171 " --> pdb=" O TYR P 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU P 200 " --> pdb=" O ASN P 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE P 173 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU P 234 " --> pdb=" O LYS P 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN P 270 " --> pdb=" O LEU P 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL P 236 " --> pdb=" O ASN P 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU P 272 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU P 238 " --> pdb=" O LEU P 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL P 301 " --> pdb=" O GLU P 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER P 336 " --> pdb=" O VAL P 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR P 303 " --> pdb=" O SER P 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN O 171 " --> pdb=" O TYR O 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU O 200 " --> pdb=" O ASN O 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE O 173 " --> pdb=" O LEU O 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU O 234 " --> pdb=" O LYS O 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN O 270 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL O 236 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU O 272 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU O 238 " --> pdb=" O LEU O 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL O 301 " --> pdb=" O GLU O 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER O 336 " --> pdb=" O VAL O 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR O 303 " --> pdb=" O SER O 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN N 171 " --> pdb=" O TYR N 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU N 200 " --> pdb=" O ASN N 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE N 173 " --> pdb=" O LEU N 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU N 234 " --> pdb=" O LYS N 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN N 270 " --> pdb=" O LEU N 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL N 236 " --> pdb=" O ASN N 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU N 272 " --> pdb=" O VAL N 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU N 238 " --> pdb=" O LEU N 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL N 301 " --> pdb=" O GLU N 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER N 336 " --> pdb=" O VAL N 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR N 303 " --> pdb=" O SER N 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN M 171 " --> pdb=" O TYR M 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU M 200 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE M 173 " --> pdb=" O LEU M 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU M 234 " --> pdb=" O LYS M 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN M 270 " --> pdb=" O LEU M 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL M 236 " --> pdb=" O ASN M 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU M 272 " --> pdb=" O VAL M 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU M 238 " --> pdb=" O LEU M 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL M 301 " --> pdb=" O GLU M 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER M 336 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR M 303 " --> pdb=" O SER M 336 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN L 171 " --> pdb=" O TYR L 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU L 200 " --> pdb=" O ASN L 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE L 173 " --> pdb=" O LEU L 200 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.537A pdb=" N LEU L 234 " --> pdb=" O LYS L 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN L 270 " --> pdb=" O LEU L 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL L 236 " --> pdb=" O ASN L 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU L 272 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU L 238 " --> pdb=" O LEU L 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL L 301 " --> pdb=" O GLU L 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER L 336 " --> pdb=" O VAL L 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR L 303 " --> pdb=" O SER L 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN K 171 " --> pdb=" O TYR K 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU K 200 " --> pdb=" O ASN K 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE K 173 " --> pdb=" O LEU K 200 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU K 234 " --> pdb=" O LYS K 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN K 270 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL K 236 " --> pdb=" O ASN K 270 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU K 272 " --> pdb=" O VAL K 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU K 238 " --> pdb=" O LEU K 272 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL K 301 " --> pdb=" O GLU K 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER K 336 " --> pdb=" O VAL K 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR K 303 " --> pdb=" O SER K 336 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN J 171 " --> pdb=" O TYR J 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU J 200 " --> pdb=" O ASN J 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE J 173 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU J 234 " --> pdb=" O LYS J 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN J 270 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL J 236 " --> pdb=" O ASN J 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU J 272 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU J 238 " --> pdb=" O LEU J 272 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL J 301 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER J 336 " --> pdb=" O VAL J 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR J 303 " --> pdb=" O SER J 336 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN I 171 " --> pdb=" O TYR I 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU I 200 " --> pdb=" O ASN I 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE I 173 " --> pdb=" O LEU I 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU I 234 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN I 270 " --> pdb=" O LEU I 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL I 236 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU I 272 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 238 " --> pdb=" O LEU I 272 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL I 301 " --> pdb=" O GLU I 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER I 336 " --> pdb=" O VAL I 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR I 303 " --> pdb=" O SER I 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN H 171 " --> pdb=" O TYR H 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU H 200 " --> pdb=" O ASN H 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE H 173 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU H 234 " --> pdb=" O LYS H 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN H 270 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL H 236 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU H 272 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU H 238 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL H 301 " --> pdb=" O GLU H 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER H 336 " --> pdb=" O VAL H 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR H 303 " --> pdb=" O SER H 336 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN G 171 " --> pdb=" O TYR G 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU G 200 " --> pdb=" O ASN G 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE G 173 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU G 234 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN G 270 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL G 236 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU G 272 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 238 " --> pdb=" O LEU G 272 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL G 301 " --> pdb=" O GLU G 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER G 336 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR G 303 " --> pdb=" O SER G 336 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN F 171 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 200 " --> pdb=" O ASN F 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE F 173 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 224 through 228 removed outlier: 6.535A pdb=" N LEU F 234 " --> pdb=" O LYS F 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN F 270 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL F 236 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU F 272 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU F 238 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL F 301 " --> pdb=" O GLU F 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER F 336 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR F 303 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN E 171 " --> pdb=" O TYR E 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU E 200 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 173 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU E 234 " --> pdb=" O LYS E 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN E 270 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 236 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU E 272 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 238 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL E 301 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER E 336 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR E 303 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 163 through 166 removed outlier: 6.487A pdb=" N ASN D 171 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU D 200 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE D 173 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU D 234 " --> pdb=" O LYS D 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN D 270 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D 236 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU D 272 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 238 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL D 301 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER D 336 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR D 303 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN C 171 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU C 200 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE C 173 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU C 234 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN C 270 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 236 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU C 272 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 238 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL C 301 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER C 336 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR C 303 " --> pdb=" O SER C 336 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN B 171 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 200 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 173 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 224 through 228 removed outlier: 6.537A pdb=" N LEU B 234 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN B 270 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 236 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 272 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 238 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL B 301 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER B 336 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 303 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN A 171 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 200 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 173 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU A 234 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN A 270 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 236 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 272 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 238 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL A 301 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER A 336 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR A 303 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 163 through 166 removed outlier: 6.485A pdb=" N ASN W 171 " --> pdb=" O TYR W 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU W 200 " --> pdb=" O ASN W 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE W 173 " --> pdb=" O LEU W 200 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 224 through 228 removed outlier: 6.535A pdb=" N LEU W 234 " --> pdb=" O LYS W 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN W 270 " --> pdb=" O LEU W 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL W 236 " --> pdb=" O ASN W 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU W 272 " --> pdb=" O VAL W 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU W 238 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL W 301 " --> pdb=" O GLU W 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER W 336 " --> pdb=" O VAL W 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR W 303 " --> pdb=" O SER W 336 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN V 171 " --> pdb=" O TYR V 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU V 200 " --> pdb=" O ASN V 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE V 173 " --> pdb=" O LEU V 200 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU V 234 " --> pdb=" O LYS V 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN V 270 " --> pdb=" O LEU V 234 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL V 236 " --> pdb=" O ASN V 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU V 272 " --> pdb=" O VAL V 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU V 238 " --> pdb=" O LEU V 272 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 292 through 297 removed outlier: 6.944A pdb=" N VAL V 301 " --> pdb=" O GLU V 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER V 336 " --> pdb=" O VAL V 301 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR V 303 " --> pdb=" O SER V 336 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN U 171 " --> pdb=" O TYR U 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU U 200 " --> pdb=" O ASN U 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE U 173 " --> pdb=" O LEU U 200 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU U 234 " --> pdb=" O LYS U 268 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN U 270 " --> pdb=" O LEU U 234 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL U 236 " --> pdb=" O ASN U 270 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU U 272 " --> pdb=" O VAL U 236 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU U 238 " --> pdb=" O LEU U 272 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL U 301 " --> pdb=" O GLU U 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER U 336 " --> pdb=" O VAL U 301 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR U 303 " --> pdb=" O SER U 336 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 163 through 166 removed outlier: 6.486A pdb=" N ASN X 171 " --> pdb=" O TYR X 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU X 200 " --> pdb=" O ASN X 171 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE X 173 " --> pdb=" O LEU X 200 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 224 through 228 removed outlier: 6.536A pdb=" N LEU X 234 " --> pdb=" O LYS X 268 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN X 270 " --> pdb=" O LEU X 234 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL X 236 " --> pdb=" O ASN X 270 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU X 272 " --> pdb=" O VAL X 236 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU X 238 " --> pdb=" O LEU X 272 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 292 through 297 removed outlier: 6.943A pdb=" N VAL X 301 " --> pdb=" O GLU X 334 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER X 336 " --> pdb=" O VAL X 301 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR X 303 " --> pdb=" O SER X 336 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 25 through 28 removed outlier: 5.909A pdb=" N SER a 26 " --> pdb=" O VAL a 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL a 59 " --> pdb=" O SER a 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE a 57 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE a 152 " --> pdb=" O ILE a 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA a 127 " --> pdb=" O ILE a 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE a 150 " --> pdb=" O ALA a 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE a 129 " --> pdb=" O SER a 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER a 148 " --> pdb=" O ILE a 129 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'b' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER b 26 " --> pdb=" O VAL b 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL b 59 " --> pdb=" O SER b 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE b 57 " --> pdb=" O LEU b 28 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'b' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE b 152 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA b 127 " --> pdb=" O ILE b 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE b 150 " --> pdb=" O ALA b 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE b 129 " --> pdb=" O SER b 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER b 148 " --> pdb=" O ILE b 129 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'c' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER c 26 " --> pdb=" O VAL c 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL c 59 " --> pdb=" O SER c 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE c 57 " --> pdb=" O LEU c 28 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE c 152 " --> pdb=" O ILE c 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA c 127 " --> pdb=" O ILE c 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE c 150 " --> pdb=" O ALA c 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE c 129 " --> pdb=" O SER c 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER c 148 " --> pdb=" O ILE c 129 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER d 26 " --> pdb=" O VAL d 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL d 59 " --> pdb=" O SER d 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE d 57 " --> pdb=" O LEU d 28 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'd' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE d 152 " --> pdb=" O ILE d 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA d 127 " --> pdb=" O ILE d 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE d 150 " --> pdb=" O ALA d 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE d 129 " --> pdb=" O SER d 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER d 148 " --> pdb=" O ILE d 129 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'e' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER e 26 " --> pdb=" O VAL e 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL e 59 " --> pdb=" O SER e 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE e 57 " --> pdb=" O LEU e 28 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'e' and resid 124 through 131 removed outlier: 6.517A pdb=" N ILE e 152 " --> pdb=" O ILE e 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA e 127 " --> pdb=" O ILE e 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE e 150 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE e 129 " --> pdb=" O SER e 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER e 148 " --> pdb=" O ILE e 129 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'f' and resid 25 through 28 removed outlier: 5.911A pdb=" N SER f 26 " --> pdb=" O VAL f 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL f 59 " --> pdb=" O SER f 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE f 57 " --> pdb=" O LEU f 28 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE f 152 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA f 127 " --> pdb=" O ILE f 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE f 150 " --> pdb=" O ALA f 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE f 129 " --> pdb=" O SER f 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER f 148 " --> pdb=" O ILE f 129 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'g' and resid 25 through 28 removed outlier: 5.909A pdb=" N SER g 26 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL g 59 " --> pdb=" O SER g 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE g 57 " --> pdb=" O LEU g 28 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'g' and resid 124 through 131 removed outlier: 6.515A pdb=" N ILE g 152 " --> pdb=" O ILE g 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA g 127 " --> pdb=" O ILE g 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE g 150 " --> pdb=" O ALA g 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE g 129 " --> pdb=" O SER g 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER g 148 " --> pdb=" O ILE g 129 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'h' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER h 26 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL h 59 " --> pdb=" O SER h 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE h 57 " --> pdb=" O LEU h 28 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'h' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE h 152 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA h 127 " --> pdb=" O ILE h 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE h 150 " --> pdb=" O ALA h 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE h 129 " --> pdb=" O SER h 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER h 148 " --> pdb=" O ILE h 129 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'i' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER i 26 " --> pdb=" O VAL i 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL i 59 " --> pdb=" O SER i 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE i 57 " --> pdb=" O LEU i 28 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'i' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE i 152 " --> pdb=" O ILE i 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA i 127 " --> pdb=" O ILE i 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE i 150 " --> pdb=" O ALA i 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE i 129 " --> pdb=" O SER i 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER i 148 " --> pdb=" O ILE i 129 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'j' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER j 26 " --> pdb=" O VAL j 59 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL j 59 " --> pdb=" O SER j 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE j 57 " --> pdb=" O LEU j 28 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'j' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE j 152 " --> pdb=" O ILE j 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA j 127 " --> pdb=" O ILE j 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE j 150 " --> pdb=" O ALA j 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE j 129 " --> pdb=" O SER j 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER j 148 " --> pdb=" O ILE j 129 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'k' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER k 26 " --> pdb=" O VAL k 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL k 59 " --> pdb=" O SER k 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE k 57 " --> pdb=" O LEU k 28 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'k' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE k 152 " --> pdb=" O ILE k 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA k 127 " --> pdb=" O ILE k 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE k 150 " --> pdb=" O ALA k 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE k 129 " --> pdb=" O SER k 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER k 148 " --> pdb=" O ILE k 129 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'l' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER l 26 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL l 59 " --> pdb=" O SER l 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE l 57 " --> pdb=" O LEU l 28 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'l' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE l 152 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA l 127 " --> pdb=" O ILE l 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE l 150 " --> pdb=" O ALA l 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE l 129 " --> pdb=" O SER l 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER l 148 " --> pdb=" O ILE l 129 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'm' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER m 26 " --> pdb=" O VAL m 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL m 59 " --> pdb=" O SER m 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE m 57 " --> pdb=" O LEU m 28 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'm' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE m 152 " --> pdb=" O ILE m 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA m 127 " --> pdb=" O ILE m 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE m 150 " --> pdb=" O ALA m 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE m 129 " --> pdb=" O SER m 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER m 148 " --> pdb=" O ILE m 129 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'n' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER n 26 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL n 59 " --> pdb=" O SER n 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE n 57 " --> pdb=" O LEU n 28 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'n' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE n 152 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA n 127 " --> pdb=" O ILE n 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE n 150 " --> pdb=" O ALA n 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE n 129 " --> pdb=" O SER n 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER n 148 " --> pdb=" O ILE n 129 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'o' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER o 26 " --> pdb=" O VAL o 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL o 59 " --> pdb=" O SER o 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE o 57 " --> pdb=" O LEU o 28 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'o' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE o 152 " --> pdb=" O ILE o 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA o 127 " --> pdb=" O ILE o 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE o 150 " --> pdb=" O ALA o 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE o 129 " --> pdb=" O SER o 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER o 148 " --> pdb=" O ILE o 129 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'p' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER p 26 " --> pdb=" O VAL p 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL p 59 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE p 57 " --> pdb=" O LEU p 28 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'p' and resid 124 through 131 removed outlier: 6.517A pdb=" N ILE p 152 " --> pdb=" O ILE p 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA p 127 " --> pdb=" O ILE p 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE p 150 " --> pdb=" O ALA p 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE p 129 " --> pdb=" O SER p 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER p 148 " --> pdb=" O ILE p 129 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'q' and resid 25 through 28 removed outlier: 5.911A pdb=" N SER q 26 " --> pdb=" O VAL q 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL q 59 " --> pdb=" O SER q 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE q 57 " --> pdb=" O LEU q 28 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'q' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE q 152 " --> pdb=" O ILE q 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA q 127 " --> pdb=" O ILE q 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE q 150 " --> pdb=" O ALA q 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE q 129 " --> pdb=" O SER q 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER q 148 " --> pdb=" O ILE q 129 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'r' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER r 26 " --> pdb=" O VAL r 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL r 59 " --> pdb=" O SER r 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE r 57 " --> pdb=" O LEU r 28 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'r' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE r 152 " --> pdb=" O ILE r 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA r 127 " --> pdb=" O ILE r 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE r 150 " --> pdb=" O ALA r 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE r 129 " --> pdb=" O SER r 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER r 148 " --> pdb=" O ILE r 129 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 's' and resid 25 through 28 removed outlier: 5.911A pdb=" N SER s 26 " --> pdb=" O VAL s 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL s 59 " --> pdb=" O SER s 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE s 57 " --> pdb=" O LEU s 28 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 's' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE s 152 " --> pdb=" O ILE s 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA s 127 " --> pdb=" O ILE s 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE s 150 " --> pdb=" O ALA s 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE s 129 " --> pdb=" O SER s 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER s 148 " --> pdb=" O ILE s 129 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 't' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER t 26 " --> pdb=" O VAL t 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL t 59 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE t 57 " --> pdb=" O LEU t 28 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 't' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE t 152 " --> pdb=" O ILE t 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA t 127 " --> pdb=" O ILE t 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE t 150 " --> pdb=" O ALA t 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE t 129 " --> pdb=" O SER t 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER t 148 " --> pdb=" O ILE t 129 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'u' and resid 25 through 28 removed outlier: 5.911A pdb=" N SER u 26 " --> pdb=" O VAL u 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL u 59 " --> pdb=" O SER u 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE u 57 " --> pdb=" O LEU u 28 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'u' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE u 152 " --> pdb=" O ILE u 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA u 127 " --> pdb=" O ILE u 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE u 150 " --> pdb=" O ALA u 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE u 129 " --> pdb=" O SER u 148 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER u 148 " --> pdb=" O ILE u 129 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'v' and resid 25 through 28 removed outlier: 5.909A pdb=" N SER v 26 " --> pdb=" O VAL v 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL v 59 " --> pdb=" O SER v 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE v 57 " --> pdb=" O LEU v 28 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'v' and resid 124 through 131 removed outlier: 6.517A pdb=" N ILE v 152 " --> pdb=" O ILE v 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA v 127 " --> pdb=" O ILE v 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE v 150 " --> pdb=" O ALA v 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE v 129 " --> pdb=" O SER v 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER v 148 " --> pdb=" O ILE v 129 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'w' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER w 26 " --> pdb=" O VAL w 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL w 59 " --> pdb=" O SER w 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE w 57 " --> pdb=" O LEU w 28 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'w' and resid 124 through 131 removed outlier: 6.516A pdb=" N ILE w 152 " --> pdb=" O ILE w 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA w 127 " --> pdb=" O ILE w 150 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE w 150 " --> pdb=" O ALA w 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE w 129 " --> pdb=" O SER w 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER w 148 " --> pdb=" O ILE w 129 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'x' and resid 25 through 28 removed outlier: 5.910A pdb=" N SER x 26 " --> pdb=" O VAL x 59 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL x 59 " --> pdb=" O SER x 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE x 57 " --> pdb=" O LEU x 28 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'x' and resid 124 through 131 removed outlier: 6.517A pdb=" N ILE x 152 " --> pdb=" O ILE x 125 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA x 127 " --> pdb=" O ILE x 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE x 150 " --> pdb=" O ALA x 127 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE x 129 " --> pdb=" O SER x 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER x 148 " --> pdb=" O ILE x 129 " (cutoff:3.500A) 3264 hydrogen bonds defined for protein. 9360 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: 30.53 Time building geometry restraints manager: 15.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23376 1.34 - 1.46: 15071 1.46 - 1.58: 33313 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 72024 Sorted by residual: bond pdb=" CG1 ILE g 185 " pdb=" CD1 ILE g 185 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.34e+00 bond pdb=" CG1 ILE t 185 " pdb=" CD1 ILE t 185 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.32e+00 bond pdb=" CG1 ILE b 185 " pdb=" CD1 ILE b 185 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.32e+00 bond pdb=" CG1 ILE l 185 " pdb=" CD1 ILE l 185 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.29e+00 bond pdb=" CG1 ILE p 185 " pdb=" CD1 ILE p 185 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.27e+00 ... (remaining 72019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 91968 1.77 - 3.54: 4440 3.54 - 5.31: 624 5.31 - 7.08: 140 7.08 - 8.85: 52 Bond angle restraints: 97224 Sorted by residual: angle pdb=" N ARG Q 161 " pdb=" CA ARG Q 161 " pdb=" C ARG Q 161 " ideal model delta sigma weight residual 114.31 107.10 7.21 1.29e+00 6.01e-01 3.13e+01 angle pdb=" N ARG C 161 " pdb=" CA ARG C 161 " pdb=" C ARG C 161 " ideal model delta sigma weight residual 114.31 107.10 7.21 1.29e+00 6.01e-01 3.13e+01 angle pdb=" N ARG W 161 " pdb=" CA ARG W 161 " pdb=" C ARG W 161 " ideal model delta sigma weight residual 114.31 107.10 7.21 1.29e+00 6.01e-01 3.13e+01 angle pdb=" N ARG I 161 " pdb=" CA ARG I 161 " pdb=" C ARG I 161 " ideal model delta sigma weight residual 114.31 107.11 7.20 1.29e+00 6.01e-01 3.11e+01 angle pdb=" N ARG J 161 " pdb=" CA ARG J 161 " pdb=" C ARG J 161 " ideal model delta sigma weight residual 114.31 107.12 7.19 1.29e+00 6.01e-01 3.11e+01 ... (remaining 97219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 42085 14.04 - 28.08: 1930 28.08 - 42.12: 484 42.12 - 56.16: 0 56.16 - 70.21: 24 Dihedral angle restraints: 44523 sinusoidal: 18363 harmonic: 26160 Sorted by residual: dihedral pdb=" CA LYS w 189 " pdb=" C LYS w 189 " pdb=" N GLU w 190 " pdb=" CA GLU w 190 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYS g 189 " pdb=" C LYS g 189 " pdb=" N GLU g 190 " pdb=" CA GLU g 190 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYS e 189 " pdb=" C LYS e 189 " pdb=" N GLU e 190 " pdb=" CA GLU e 190 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 44520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7321 0.048 - 0.096: 2695 0.096 - 0.143: 1034 0.143 - 0.191: 110 0.191 - 0.239: 48 Chirality restraints: 11208 Sorted by residual: chirality pdb=" CA LEU u 78 " pdb=" N LEU u 78 " pdb=" C LEU u 78 " pdb=" CB LEU u 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LEU w 78 " pdb=" N LEU w 78 " pdb=" C LEU w 78 " pdb=" CB LEU w 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LEU h 78 " pdb=" N LEU h 78 " pdb=" C LEU h 78 " pdb=" CB LEU h 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 11205 not shown) Planarity restraints: 12456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS O 160 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C LYS O 160 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS O 160 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG O 161 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 160 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LYS Q 160 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS Q 160 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG Q 161 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 160 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C LYS V 160 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS V 160 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG V 161 " 0.012 2.00e-02 2.50e+03 ... (remaining 12453 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 687 2.61 - 3.18: 56728 3.18 - 3.75: 100214 3.75 - 4.33: 141527 4.33 - 4.90: 240411 Nonbonded interactions: 539567 Sorted by model distance: nonbonded pdb=" SG CYS E 170 " pdb=" SG CYS E 196 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS N 170 " pdb=" SG CYS N 196 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS L 170 " pdb=" SG CYS L 196 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS R 170 " pdb=" SG CYS R 196 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 170 " pdb=" SG CYS D 196 " model vdw 2.033 3.760 ... (remaining 539562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.980 Check model and map are aligned: 0.390 Set scattering table: 0.510 Process input model: 106.710 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.850 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: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 121.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 0.081 72024 Z= 0.562 Angle : 0.890 8.851 97224 Z= 0.494 Chirality : 0.058 0.239 11208 Planarity : 0.006 0.047 12456 Dihedral : 9.101 70.205 27528 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.08), residues: 8688 helix: -1.59 (0.07), residues: 3432 sheet: -0.38 (0.11), residues: 2088 loop : -3.00 (0.09), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.007 TRP G 183 HIS 0.007 0.003 HIS p 43 PHE 0.011 0.002 PHE D 219 TYR 0.024 0.003 TYR J 332 ARG 0.008 0.001 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2422 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2422 time to evaluate : 7.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 215 GLN cc_start: 0.8906 (tt0) cc_final: 0.8660 (tt0) REVERT: S 252 LYS cc_start: 0.8351 (ttpm) cc_final: 0.7916 (ttmt) REVERT: S 302 THR cc_start: 0.9049 (t) cc_final: 0.8736 (p) REVERT: S 304 SER cc_start: 0.9095 (t) cc_final: 0.8855 (p) REVERT: S 330 ASP cc_start: 0.8183 (t70) cc_final: 0.7975 (t0) REVERT: T 170 CYS cc_start: 0.6231 (t) cc_final: 0.5907 (t) REVERT: T 304 SER cc_start: 0.9101 (t) cc_final: 0.8875 (p) REVERT: Q 215 GLN cc_start: 0.8939 (tt0) cc_final: 0.8603 (tt0) REVERT: Q 274 ASP cc_start: 0.8305 (m-30) cc_final: 0.8000 (m-30) REVERT: P 210 GLN cc_start: 0.8503 (tt0) cc_final: 0.8303 (tt0) REVERT: P 273 SER cc_start: 0.8946 (t) cc_final: 0.8483 (t) REVERT: P 275 HIS cc_start: 0.7786 (m-70) cc_final: 0.7560 (m-70) REVERT: P 322 SER cc_start: 0.9373 (t) cc_final: 0.9098 (t) REVERT: P 330 ASP cc_start: 0.8063 (t70) cc_final: 0.7843 (t0) REVERT: O 275 HIS cc_start: 0.7763 (m-70) cc_final: 0.7518 (m-70) REVERT: O 330 ASP cc_start: 0.8225 (t70) cc_final: 0.8004 (t0) REVERT: M 322 SER cc_start: 0.9393 (t) cc_final: 0.9174 (t) REVERT: M 330 ASP cc_start: 0.8283 (t70) cc_final: 0.7932 (t0) REVERT: L 275 HIS cc_start: 0.7858 (m-70) cc_final: 0.7446 (m-70) REVERT: L 286 THR cc_start: 0.9517 (t) cc_final: 0.9161 (m) REVERT: L 330 ASP cc_start: 0.7905 (t70) cc_final: 0.7646 (t0) REVERT: K 167 THR cc_start: 0.8440 (p) cc_final: 0.8214 (p) REVERT: K 215 GLN cc_start: 0.8952 (tt0) cc_final: 0.8520 (tt0) REVERT: K 274 ASP cc_start: 0.8346 (m-30) cc_final: 0.7775 (m-30) REVERT: K 275 HIS cc_start: 0.7951 (m-70) cc_final: 0.7480 (m-70) REVERT: J 327 ILE cc_start: 0.9238 (mt) cc_final: 0.9004 (mt) REVERT: I 159 ASP cc_start: 0.6560 (t0) cc_final: 0.6238 (t0) REVERT: I 166 ASN cc_start: 0.8600 (t0) cc_final: 0.8083 (t0) REVERT: H 330 ASP cc_start: 0.7896 (t70) cc_final: 0.7537 (t0) REVERT: G 159 ASP cc_start: 0.6770 (t0) cc_final: 0.6544 (t0) REVERT: G 206 ILE cc_start: 0.9359 (mt) cc_final: 0.9121 (mm) REVERT: F 274 ASP cc_start: 0.8348 (m-30) cc_final: 0.7834 (m-30) REVERT: F 275 HIS cc_start: 0.7588 (m-70) cc_final: 0.7250 (m-70) REVERT: E 179 ASN cc_start: 0.7991 (t0) cc_final: 0.7629 (t0) REVERT: E 260 GLU cc_start: 0.7932 (tp30) cc_final: 0.7594 (tp30) REVERT: E 311 ASP cc_start: 0.8280 (m-30) cc_final: 0.7933 (m-30) REVERT: D 311 ASP cc_start: 0.8366 (m-30) cc_final: 0.8043 (m-30) REVERT: A 206 ILE cc_start: 0.9381 (mt) cc_final: 0.9179 (mm) REVERT: A 302 THR cc_start: 0.9013 (t) cc_final: 0.8784 (p) REVERT: V 176 GLU cc_start: 0.7194 (tt0) cc_final: 0.6865 (tt0) REVERT: V 215 GLN cc_start: 0.8997 (tt0) cc_final: 0.8662 (tt0) REVERT: V 274 ASP cc_start: 0.8452 (m-30) cc_final: 0.8057 (m-30) REVERT: V 275 HIS cc_start: 0.7751 (m-70) cc_final: 0.7406 (m-70) REVERT: X 330 ASP cc_start: 0.8127 (t70) cc_final: 0.7914 (t0) REVERT: a 65 THR cc_start: 0.8946 (p) cc_final: 0.8713 (p) REVERT: b 111 GLU cc_start: 0.8127 (tt0) cc_final: 0.7873 (tt0) REVERT: b 172 ASN cc_start: 0.8744 (m110) cc_final: 0.8434 (m110) REVERT: c 61 VAL cc_start: 0.8630 (t) cc_final: 0.8408 (p) REVERT: c 103 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8757 (ttpt) REVERT: c 189 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8657 (ttpp) REVERT: d 71 ASP cc_start: 0.8864 (t70) cc_final: 0.8540 (t0) REVERT: d 160 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6706 (mm-30) REVERT: e 103 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8520 (ttmt) REVERT: e 107 TYR cc_start: 0.8565 (m-80) cc_final: 0.8364 (m-80) REVERT: e 114 LEU cc_start: 0.9467 (mt) cc_final: 0.8901 (mt) REVERT: e 152 ILE cc_start: 0.8939 (mt) cc_final: 0.8734 (mt) REVERT: e 171 LYS cc_start: 0.9066 (tmtm) cc_final: 0.8789 (tptp) REVERT: e 194 TYR cc_start: 0.8669 (m-80) cc_final: 0.8280 (m-80) REVERT: f 30 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8343 (mm-40) REVERT: f 49 LYS cc_start: 0.8227 (mtpt) cc_final: 0.8001 (mtpp) REVERT: f 111 GLU cc_start: 0.7516 (tt0) cc_final: 0.7300 (tt0) REVERT: f 194 TYR cc_start: 0.8622 (m-80) cc_final: 0.8354 (m-80) REVERT: g 194 TYR cc_start: 0.8654 (m-80) cc_final: 0.8068 (m-80) REVERT: h 65 THR cc_start: 0.8852 (p) cc_final: 0.8622 (p) REVERT: h 107 TYR cc_start: 0.9069 (m-80) cc_final: 0.8829 (m-10) REVERT: h 176 ASP cc_start: 0.8041 (p0) cc_final: 0.7819 (p0) REVERT: i 65 THR cc_start: 0.8845 (p) cc_final: 0.8611 (p) REVERT: i 189 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8368 (ttpp) REVERT: i 194 TYR cc_start: 0.8522 (m-80) cc_final: 0.8118 (m-80) REVERT: k 46 THR cc_start: 0.8720 (p) cc_final: 0.8400 (p) REVERT: k 103 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8613 (ttmt) REVERT: l 26 SER cc_start: 0.9021 (p) cc_final: 0.8820 (t) REVERT: l 194 TYR cc_start: 0.8552 (m-80) cc_final: 0.8349 (m-80) REVERT: n 26 SER cc_start: 0.9109 (p) cc_final: 0.8893 (t) REVERT: n 91 PRO cc_start: 0.8702 (Cg_exo) cc_final: 0.8459 (Cg_endo) REVERT: n 107 TYR cc_start: 0.9047 (m-80) cc_final: 0.8627 (m-10) REVERT: n 112 GLN cc_start: 0.8697 (mt0) cc_final: 0.8377 (mt0) REVERT: n 176 ASP cc_start: 0.8063 (p0) cc_final: 0.7780 (p0) REVERT: o 26 SER cc_start: 0.8902 (p) cc_final: 0.8515 (t) REVERT: o 189 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8196 (ttpp) REVERT: o 195 THR cc_start: 0.8836 (p) cc_final: 0.8481 (p) REVERT: p 60 GLN cc_start: 0.8209 (mt0) cc_final: 0.7939 (mt0) REVERT: p 103 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8778 (ttmt) REVERT: p 114 LEU cc_start: 0.9587 (mt) cc_final: 0.9342 (mt) REVERT: p 171 LYS cc_start: 0.9159 (tmtm) cc_final: 0.8938 (tptp) REVERT: p 189 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8168 (ttpt) REVERT: q 21 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7576 (mmm-85) REVERT: r 189 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8222 (ttpp) REVERT: r 196 ASN cc_start: 0.8976 (m-40) cc_final: 0.8703 (m110) REVERT: s 65 THR cc_start: 0.8995 (p) cc_final: 0.8728 (p) REVERT: s 108 SER cc_start: 0.9138 (t) cc_final: 0.8852 (p) REVERT: t 26 SER cc_start: 0.9047 (p) cc_final: 0.8545 (t) REVERT: t 107 TYR cc_start: 0.9055 (m-80) cc_final: 0.8523 (m-10) REVERT: t 176 ASP cc_start: 0.8077 (p0) cc_final: 0.7767 (p0) REVERT: t 189 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8358 (ttpp) REVERT: u 30 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8285 (mm-40) REVERT: u 189 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8461 (ttpp) REVERT: v 65 THR cc_start: 0.8789 (p) cc_final: 0.8498 (p) REVERT: v 107 TYR cc_start: 0.9045 (m-80) cc_final: 0.8806 (m-80) REVERT: v 111 GLU cc_start: 0.7500 (tt0) cc_final: 0.7258 (tt0) REVERT: v 189 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8762 (ttpp) REVERT: w 100 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8255 (ttm110) REVERT: w 160 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7038 (mm-30) REVERT: x 103 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8682 (ttmt) REVERT: x 111 GLU cc_start: 0.7869 (tt0) cc_final: 0.7633 (tt0) REVERT: x 114 LEU cc_start: 0.9521 (mt) cc_final: 0.9235 (mt) REVERT: x 189 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8306 (ttpt) outliers start: 0 outliers final: 0 residues processed: 2422 average time/residue: 0.7621 time to fit residues: 2978.1353 Evaluate side-chains 1691 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1691 time to evaluate : 6.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 0.5980 chunk 636 optimal weight: 2.9990 chunk 353 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 429 optimal weight: 0.9980 chunk 340 optimal weight: 0.9990 chunk 658 optimal weight: 0.2980 chunk 254 optimal weight: 0.8980 chunk 400 optimal weight: 1.9990 chunk 490 optimal weight: 0.0870 chunk 762 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 171 ASN S 210 GLN S 318 ASN T 210 GLN T 318 ASN R 318 ASN R 331 GLN Q 318 ASN P 171 ASN P 318 ASN O 318 ASN M 210 GLN M 318 ASN K 318 ASN J 215 GLN G 179 ASN G 291 GLN F 210 GLN D 171 ASN B 318 ASN A 210 GLN A 318 ASN W 171 ASN W 318 ASN V 171 ASN V 318 ASN U 318 ASN U 331 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 ASN b 44 ASN b 60 GLN ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 GLN ** f 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 60 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 27 ASN m 34 ASN ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 ASN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN ** p 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 ASN q 55 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 112 GLN ** r 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 GLN s 88 GLN ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 172 ASN s 196 ASN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 196 ASN ** u 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 112 GLN ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 72024 Z= 0.194 Angle : 0.532 7.444 97224 Z= 0.284 Chirality : 0.044 0.207 11208 Planarity : 0.003 0.031 12456 Dihedral : 4.599 24.665 9600 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.67 % Allowed : 11.17 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.09), residues: 8688 helix: 1.12 (0.08), residues: 3408 sheet: -0.15 (0.11), residues: 2208 loop : -2.71 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP R 183 HIS 0.003 0.001 HIS e 43 PHE 0.011 0.001 PHE F 193 TYR 0.016 0.001 TYR q 194 ARG 0.006 0.001 ARG W 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2235 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 2100 time to evaluate : 6.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 176 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7731 (tp30) REVERT: S 249 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6732 (tp30) REVERT: T 170 CYS cc_start: 0.8157 (t) cc_final: 0.7510 (t) REVERT: T 196 CYS cc_start: 0.7023 (t) cc_final: 0.6603 (t) REVERT: R 275 HIS cc_start: 0.7852 (m-70) cc_final: 0.7622 (m-70) REVERT: Q 274 ASP cc_start: 0.8284 (m-30) cc_final: 0.7659 (m-30) REVERT: P 176 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7207 (tp30) REVERT: P 275 HIS cc_start: 0.7759 (m-70) cc_final: 0.7489 (m-70) REVERT: O 166 ASN cc_start: 0.8771 (t0) cc_final: 0.8384 (t0) REVERT: O 275 HIS cc_start: 0.7679 (m-70) cc_final: 0.7462 (m-70) REVERT: N 206 ILE cc_start: 0.9459 (mm) cc_final: 0.9123 (mt) REVERT: M 159 ASP cc_start: 0.5754 (t0) cc_final: 0.5435 (t0) REVERT: M 176 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7580 (tp30) REVERT: M 223 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8741 (m-10) REVERT: L 176 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7383 (tp30) REVERT: L 263 TYR cc_start: 0.9003 (p90) cc_final: 0.8745 (p90) REVERT: L 275 HIS cc_start: 0.7809 (m-70) cc_final: 0.7468 (m-70) REVERT: L 330 ASP cc_start: 0.7829 (t70) cc_final: 0.7490 (t0) REVERT: K 205 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7923 (mm-30) REVERT: K 274 ASP cc_start: 0.8415 (m-30) cc_final: 0.7924 (m-30) REVERT: K 275 HIS cc_start: 0.7799 (m-70) cc_final: 0.7402 (m-70) REVERT: J 166 ASN cc_start: 0.8875 (t0) cc_final: 0.8653 (t0) REVERT: J 278 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7907 (mtp180) REVERT: J 331 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7742 (mt0) REVERT: I 166 ASN cc_start: 0.8491 (t0) cc_final: 0.8013 (t0) REVERT: H 220 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8849 (mt) REVERT: G 205 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7619 (mm-30) REVERT: G 206 ILE cc_start: 0.9344 (mt) cc_final: 0.9102 (mt) REVERT: G 223 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: F 176 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7699 (tp30) REVERT: F 210 GLN cc_start: 0.8511 (tt0) cc_final: 0.8280 (tt0) REVERT: E 179 ASN cc_start: 0.8209 (t0) cc_final: 0.7830 (t0) REVERT: E 205 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8127 (mm-30) REVERT: E 211 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7808 (tt0) REVERT: E 260 GLU cc_start: 0.7887 (tp30) cc_final: 0.7681 (tp30) REVERT: E 307 GLU cc_start: 0.6758 (tt0) cc_final: 0.6548 (tt0) REVERT: E 311 ASP cc_start: 0.8164 (m-30) cc_final: 0.7941 (m-30) REVERT: D 205 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 210 GLN cc_start: 0.8353 (tt0) cc_final: 0.8081 (tt0) REVERT: D 229 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8973 (p) REVERT: D 302 THR cc_start: 0.9222 (t) cc_final: 0.8818 (p) REVERT: C 166 ASN cc_start: 0.8714 (t0) cc_final: 0.8458 (t0) REVERT: B 206 ILE cc_start: 0.9485 (mm) cc_final: 0.9178 (mt) REVERT: A 166 ASN cc_start: 0.8852 (t0) cc_final: 0.8648 (t0) REVERT: A 176 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7749 (tp30) REVERT: A 206 ILE cc_start: 0.9346 (mt) cc_final: 0.8979 (mp) REVERT: V 205 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7893 (mm-30) REVERT: V 215 GLN cc_start: 0.8960 (tt0) cc_final: 0.8518 (tt0) REVERT: V 241 GLU cc_start: 0.7425 (mp0) cc_final: 0.6846 (mp0) REVERT: V 274 ASP cc_start: 0.8284 (m-30) cc_final: 0.7585 (m-30) REVERT: V 275 HIS cc_start: 0.7686 (m-70) cc_final: 0.7276 (m-70) REVERT: U 176 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7642 (tp30) REVERT: U 263 TYR cc_start: 0.9209 (p90) cc_final: 0.8740 (p90) REVERT: X 170 CYS cc_start: 0.7965 (t) cc_final: 0.6325 (t) REVERT: X 302 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8515 (p) REVERT: a 21 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7205 (mmt90) REVERT: a 103 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8712 (ttpt) REVERT: b 60 GLN cc_start: 0.8442 (mt0) cc_final: 0.8216 (mt0) REVERT: b 128 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8647 (mmtp) REVERT: b 176 ASP cc_start: 0.8002 (p0) cc_final: 0.7634 (p0) REVERT: b 194 TYR cc_start: 0.8706 (m-80) cc_final: 0.8317 (m-80) REVERT: c 42 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8461 (ttp-110) REVERT: c 74 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7854 (ttp80) REVERT: c 189 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8587 (ttpp) REVERT: d 71 ASP cc_start: 0.8679 (t70) cc_final: 0.8380 (t0) REVERT: d 160 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6826 (mm-30) REVERT: e 60 GLN cc_start: 0.8513 (mt0) cc_final: 0.8248 (mt0) REVERT: f 37 ILE cc_start: 0.9430 (mt) cc_final: 0.9170 (mt) REVERT: g 60 GLN cc_start: 0.8335 (mt0) cc_final: 0.8054 (mt0) REVERT: g 176 ASP cc_start: 0.7779 (p0) cc_final: 0.7514 (p0) REVERT: g 194 TYR cc_start: 0.8557 (m-80) cc_final: 0.8153 (m-80) REVERT: h 107 TYR cc_start: 0.9168 (m-80) cc_final: 0.8825 (m-10) REVERT: h 176 ASP cc_start: 0.7996 (p0) cc_final: 0.7669 (p0) REVERT: i 113 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8470 (ttt90) REVERT: i 194 TYR cc_start: 0.8588 (m-80) cc_final: 0.8289 (m-80) REVERT: j 22 GLU cc_start: 0.7309 (mp0) cc_final: 0.7097 (mp0) REVERT: j 114 LEU cc_start: 0.9469 (mt) cc_final: 0.9171 (mt) REVERT: k 171 LYS cc_start: 0.9289 (tptp) cc_final: 0.9062 (tptp) REVERT: k 194 TYR cc_start: 0.8593 (m-80) cc_final: 0.8293 (m-80) REVERT: l 103 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8871 (mtmt) REVERT: l 176 ASP cc_start: 0.7908 (p0) cc_final: 0.7608 (p0) REVERT: l 189 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8353 (ttpp) REVERT: l 194 TYR cc_start: 0.8472 (m-80) cc_final: 0.8203 (m-80) REVERT: m 194 TYR cc_start: 0.8658 (m-80) cc_final: 0.8360 (m-80) REVERT: n 26 SER cc_start: 0.9106 (p) cc_final: 0.8874 (t) REVERT: n 107 TYR cc_start: 0.9153 (m-80) cc_final: 0.8919 (m-10) REVERT: n 176 ASP cc_start: 0.7962 (p0) cc_final: 0.7558 (p0) REVERT: o 26 SER cc_start: 0.9073 (p) cc_final: 0.8789 (t) REVERT: o 189 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8352 (ttpp) REVERT: o 194 TYR cc_start: 0.8577 (m-80) cc_final: 0.8124 (m-80) REVERT: p 44 ASN cc_start: 0.9459 (t0) cc_final: 0.9093 (t0) REVERT: q 114 LEU cc_start: 0.9549 (mt) cc_final: 0.9081 (mt) REVERT: r 128 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8762 (mmtm) REVERT: r 176 ASP cc_start: 0.7985 (p0) cc_final: 0.7648 (p0) REVERT: s 21 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7266 (mmt90) REVERT: s 27 ASN cc_start: 0.8688 (t0) cc_final: 0.8442 (t0) REVERT: s 72 LEU cc_start: 0.9045 (mt) cc_final: 0.8724 (mt) REVERT: s 103 LYS cc_start: 0.8821 (tttt) cc_final: 0.8533 (mtmt) REVERT: t 26 SER cc_start: 0.9044 (p) cc_final: 0.8729 (t) REVERT: t 107 TYR cc_start: 0.9219 (m-80) cc_final: 0.8840 (m-10) REVERT: t 176 ASP cc_start: 0.7988 (p0) cc_final: 0.7522 (p0) REVERT: u 74 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8096 (ttp80) REVERT: u 113 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8704 (ttt90) REVERT: u 189 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8553 (ttpp) REVERT: w 100 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8223 (ttm110) REVERT: x 30 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8353 (mm-40) REVERT: x 103 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8682 (ttmt) outliers start: 135 outliers final: 65 residues processed: 2176 average time/residue: 0.7563 time to fit residues: 2686.3651 Evaluate side-chains 1778 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1708 time to evaluate : 8.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 247 ASP Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain Q residue 174 LEU Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 206 ILE Chi-restraints excluded: chain W residue 250 LEU Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 273 SER Chi-restraints excluded: chain U residue 247 ASP Chi-restraints excluded: chain X residue 229 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 155 SER Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 82 GLU Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 41 GLU Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain k residue 186 LEU Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 186 LEU Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 41 GLU Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 155 SER Chi-restraints excluded: chain q residue 186 LEU Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain x residue 41 GLU Chi-restraints excluded: chain x residue 61 VAL Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 634 optimal weight: 1.9990 chunk 519 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 764 optimal weight: 2.9990 chunk 825 optimal weight: 0.7980 chunk 680 optimal weight: 1.9990 chunk 757 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 613 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 ASN R 331 GLN Q 275 HIS N 171 ASN N 318 ASN L 171 ASN K 171 ASN I 318 ASN H 171 ASN G 210 GLN G 275 HIS G 291 GLN F 171 ASN E 318 ASN D 275 HIS B 171 ASN U 171 ASN ** U 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 275 HIS ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** j 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN l 30 GLN l 88 GLN ** l 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 ASN m 88 GLN ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 GLN v 112 GLN ** v 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 112 GLN ** w 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 112 GLN ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 72024 Z= 0.409 Angle : 0.631 7.989 97224 Z= 0.331 Chirality : 0.047 0.167 11208 Planarity : 0.003 0.033 12456 Dihedral : 4.695 25.834 9600 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.72 % Allowed : 13.22 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.09), residues: 8688 helix: 1.74 (0.09), residues: 3408 sheet: -0.17 (0.11), residues: 2208 loop : -2.48 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 183 HIS 0.004 0.001 HIS N 275 PHE 0.012 0.001 PHE F 193 TYR 0.016 0.002 TYR q 194 ARG 0.006 0.001 ARG H 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2006 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1787 time to evaluate : 7.328 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: S 176 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7833 (tp30) REVERT: S 238 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9062 (pp) REVERT: T 170 CYS cc_start: 0.8037 (t) cc_final: 0.7529 (m) REVERT: T 196 CYS cc_start: 0.7210 (t) cc_final: 0.6099 (t) REVERT: T 238 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9065 (pp) REVERT: Q 205 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: Q 274 ASP cc_start: 0.8293 (m-30) cc_final: 0.8086 (m-30) REVERT: P 238 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8931 (pp) REVERT: P 275 HIS cc_start: 0.7932 (m-70) cc_final: 0.7613 (m-70) REVERT: O 166 ASN cc_start: 0.8814 (t0) cc_final: 0.8425 (t0) REVERT: N 161 ARG cc_start: 0.8749 (ttp-170) cc_final: 0.8390 (ttp-170) REVERT: M 176 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7750 (tp30) REVERT: M 223 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8894 (m-10) REVERT: M 238 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8963 (pp) REVERT: L 161 ARG cc_start: 0.8892 (ttp-170) cc_final: 0.8676 (ttp-170) REVERT: L 176 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7577 (tp30) REVERT: L 238 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8993 (pp) REVERT: K 179 ASN cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: K 205 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8302 (mm-30) REVERT: K 223 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8825 (m-10) REVERT: K 274 ASP cc_start: 0.8408 (m-30) cc_final: 0.7743 (m-30) REVERT: K 275 HIS cc_start: 0.7877 (m-70) cc_final: 0.7540 (m-70) REVERT: J 238 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8911 (pp) REVERT: J 278 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8055 (mtp180) REVERT: J 327 ILE cc_start: 0.9258 (mt) cc_final: 0.9042 (mt) REVERT: I 166 ASN cc_start: 0.8796 (t0) cc_final: 0.8458 (t0) REVERT: G 166 ASN cc_start: 0.8830 (t0) cc_final: 0.8602 (t0) REVERT: G 223 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8900 (m-10) REVERT: F 176 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7621 (tp30) REVERT: F 196 CYS cc_start: 0.7094 (t) cc_final: 0.6806 (t) REVERT: F 238 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8989 (pp) REVERT: F 274 ASP cc_start: 0.8623 (m-30) cc_final: 0.8163 (m-30) REVERT: E 211 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8009 (tt0) REVERT: E 273 SER cc_start: 0.8988 (t) cc_final: 0.8770 (p) REVERT: E 274 ASP cc_start: 0.8518 (m-30) cc_final: 0.8217 (m-30) REVERT: E 275 HIS cc_start: 0.7803 (m-70) cc_final: 0.7435 (m-70) REVERT: E 296 CYS cc_start: 0.7385 (t) cc_final: 0.7167 (t) REVERT: E 307 GLU cc_start: 0.6794 (tt0) cc_final: 0.6582 (tt0) REVERT: D 263 TYR cc_start: 0.9063 (p90) cc_final: 0.8854 (p90) REVERT: D 302 THR cc_start: 0.9284 (t) cc_final: 0.8832 (p) REVERT: C 166 ASN cc_start: 0.8811 (t0) cc_final: 0.8524 (t0) REVERT: A 166 ASN cc_start: 0.8969 (t0) cc_final: 0.8763 (t0) REVERT: A 176 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7920 (tp30) REVERT: A 228 VAL cc_start: 0.9182 (t) cc_final: 0.8900 (m) REVERT: A 238 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8987 (pp) REVERT: V 275 HIS cc_start: 0.7833 (m-70) cc_final: 0.7472 (m-70) REVERT: U 161 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8623 (ttp80) REVERT: U 238 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8926 (pp) REVERT: U 275 HIS cc_start: 0.7749 (m-70) cc_final: 0.7456 (m-70) REVERT: X 166 ASN cc_start: 0.8837 (t0) cc_final: 0.8629 (t0) REVERT: a 113 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8473 (ttp80) REVERT: b 176 ASP cc_start: 0.8251 (p0) cc_final: 0.7741 (p0) REVERT: c 74 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7878 (ttp80) REVERT: c 189 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8653 (ttpp) REVERT: c 194 TYR cc_start: 0.8553 (m-80) cc_final: 0.8219 (m-80) REVERT: d 22 GLU cc_start: 0.7403 (mp0) cc_final: 0.7011 (mp0) REVERT: d 160 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7164 (mm-30) REVERT: e 46 THR cc_start: 0.9064 (p) cc_final: 0.8858 (p) REVERT: e 194 TYR cc_start: 0.8676 (m-80) cc_final: 0.8469 (m-80) REVERT: f 48 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7707 (mmt180) REVERT: f 176 ASP cc_start: 0.8057 (p0) cc_final: 0.7808 (p0) REVERT: g 113 ARG cc_start: 0.8612 (ttt180) cc_final: 0.8282 (ttt90) REVERT: g 176 ASP cc_start: 0.7990 (p0) cc_final: 0.7761 (p0) REVERT: g 194 TYR cc_start: 0.8575 (m-80) cc_final: 0.8074 (m-80) REVERT: h 107 TYR cc_start: 0.9215 (m-80) cc_final: 0.8937 (m-10) REVERT: h 112 GLN cc_start: 0.8783 (mt0) cc_final: 0.8523 (mt0) REVERT: h 176 ASP cc_start: 0.8084 (p0) cc_final: 0.7721 (p0) REVERT: i 26 SER cc_start: 0.9051 (p) cc_final: 0.8741 (t) REVERT: i 194 TYR cc_start: 0.8785 (m-80) cc_final: 0.8332 (m-80) REVERT: j 44 ASN cc_start: 0.9522 (t0) cc_final: 0.8941 (t0) REVERT: k 171 LYS cc_start: 0.9355 (tptp) cc_final: 0.9123 (tptp) REVERT: l 103 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8874 (ttmt) REVERT: l 128 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8837 (mmtm) REVERT: l 176 ASP cc_start: 0.8040 (p0) cc_final: 0.7684 (p0) REVERT: m 46 THR cc_start: 0.8992 (p) cc_final: 0.8670 (p) REVERT: m 113 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8175 (ttt180) REVERT: m 176 ASP cc_start: 0.8065 (p0) cc_final: 0.7852 (p0) REVERT: m 194 TYR cc_start: 0.8706 (m-80) cc_final: 0.8232 (m-80) REVERT: n 107 TYR cc_start: 0.9198 (m-80) cc_final: 0.8986 (m-10) REVERT: n 112 GLN cc_start: 0.8846 (mt0) cc_final: 0.8602 (mt0) REVERT: n 176 ASP cc_start: 0.8035 (p0) cc_final: 0.7591 (p0) REVERT: o 26 SER cc_start: 0.9089 (p) cc_final: 0.8819 (t) REVERT: o 189 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8634 (ttpp) REVERT: o 194 TYR cc_start: 0.8751 (m-80) cc_final: 0.8315 (m-80) REVERT: p 22 GLU cc_start: 0.7422 (mp0) cc_final: 0.7174 (mp0) REVERT: p 60 GLN cc_start: 0.8383 (mt0) cc_final: 0.8150 (mt0) REVERT: q 113 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: q 168 ARG cc_start: 0.8898 (tpt170) cc_final: 0.8676 (tpt90) REVERT: q 194 TYR cc_start: 0.8623 (m-80) cc_final: 0.8253 (m-80) REVERT: r 176 ASP cc_start: 0.7975 (p0) cc_final: 0.7601 (p0) REVERT: s 176 ASP cc_start: 0.8146 (p0) cc_final: 0.7945 (p0) REVERT: t 107 TYR cc_start: 0.9216 (m-80) cc_final: 0.8928 (m-10) REVERT: t 112 GLN cc_start: 0.8805 (mt0) cc_final: 0.8558 (mt0) REVERT: t 176 ASP cc_start: 0.8095 (p0) cc_final: 0.7666 (p0) REVERT: u 26 SER cc_start: 0.9036 (p) cc_final: 0.8770 (t) REVERT: u 74 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8124 (ttp80) REVERT: u 113 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8708 (ttt90) REVERT: u 189 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8573 (ttpp) REVERT: v 113 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8590 (ttt90) REVERT: v 128 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8762 (mmtm) REVERT: v 191 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6920 (mm-30) REVERT: w 60 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: w 100 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8212 (ttm110) REVERT: w 176 ASP cc_start: 0.8245 (p0) cc_final: 0.8019 (p0) REVERT: w 194 TYR cc_start: 0.8707 (m-80) cc_final: 0.8326 (m-80) REVERT: x 22 GLU cc_start: 0.7646 (mp0) cc_final: 0.7420 (mp0) REVERT: x 30 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8307 (mm-40) REVERT: x 74 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8048 (ttp80) REVERT: x 103 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8787 (ttmt) REVERT: x 191 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7188 (mm-30) outliers start: 219 outliers final: 145 residues processed: 1932 average time/residue: 0.7830 time to fit residues: 2454.5419 Evaluate side-chains 1763 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1600 time to evaluate : 6.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 294 GLU Chi-restraints excluded: chain R residue 223 TYR Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain Q residue 174 LEU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 248 THR Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 307 GLU Chi-restraints excluded: chain K residue 223 TYR Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 250 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 273 SER Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 267 ILE Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain U residue 306 ARG Chi-restraints excluded: chain U residue 338 LEU Chi-restraints excluded: chain X residue 229 SER Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 155 SER Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 89 MET Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 41 GLU Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 46 THR Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 41 GLU Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 58 SER Chi-restraints excluded: chain q residue 84 VAL Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 155 SER Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 58 SER Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain u residue 193 VAL Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 113 ARG Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 60 GLN Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain x residue 41 GLU Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 108 SER Chi-restraints excluded: chain x residue 155 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 0.7980 chunk 574 optimal weight: 0.1980 chunk 396 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 364 optimal weight: 1.9990 chunk 513 optimal weight: 0.9980 chunk 766 optimal weight: 2.9990 chunk 811 optimal weight: 0.6980 chunk 400 optimal weight: 0.6980 chunk 726 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 171 ASN J 171 ASN I 210 GLN G 275 HIS G 299 ASN U 331 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 112 GLN ** c 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** j 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 GLN p 88 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 172 ASN ** w 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 112 GLN ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 72024 Z= 0.208 Angle : 0.515 6.135 97224 Z= 0.274 Chirality : 0.044 0.149 11208 Planarity : 0.003 0.025 12456 Dihedral : 4.340 25.181 9600 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.84 % Allowed : 14.22 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8688 helix: 2.11 (0.09), residues: 3408 sheet: 0.12 (0.11), residues: 2160 loop : -2.36 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 183 HIS 0.002 0.001 HIS f 43 PHE 0.010 0.001 PHE F 193 TYR 0.013 0.001 TYR q 194 ARG 0.006 0.001 ARG R 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2095 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1866 time to evaluate : 6.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 159 ASP cc_start: 0.5424 (t0) cc_final: 0.5111 (t0) REVERT: S 275 HIS cc_start: 0.7773 (m-70) cc_final: 0.7543 (m-70) REVERT: T 170 CYS cc_start: 0.7952 (t) cc_final: 0.7522 (m) REVERT: T 196 CYS cc_start: 0.7113 (t) cc_final: 0.6048 (t) REVERT: T 206 ILE cc_start: 0.9426 (mt) cc_final: 0.9113 (mt) REVERT: T 263 TYR cc_start: 0.9082 (p90) cc_final: 0.8720 (p90) REVERT: R 238 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8974 (pp) REVERT: R 274 ASP cc_start: 0.8646 (m-30) cc_final: 0.8405 (m-30) REVERT: R 330 ASP cc_start: 0.8201 (t70) cc_final: 0.7949 (t0) REVERT: Q 274 ASP cc_start: 0.8249 (m-30) cc_final: 0.7878 (m-30) REVERT: Q 275 HIS cc_start: 0.7880 (m-70) cc_final: 0.7582 (m-70) REVERT: P 176 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7446 (tp30) REVERT: P 223 TYR cc_start: 0.8985 (m-80) cc_final: 0.8777 (m-80) REVERT: P 238 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8863 (pp) REVERT: P 251 ASP cc_start: 0.7843 (m-30) cc_final: 0.7611 (m-30) REVERT: P 275 HIS cc_start: 0.7813 (m-70) cc_final: 0.7484 (m-70) REVERT: O 166 ASN cc_start: 0.8640 (t0) cc_final: 0.8187 (t0) REVERT: O 238 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8983 (pp) REVERT: N 205 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7654 (mm-30) REVERT: N 238 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8907 (pp) REVERT: N 251 ASP cc_start: 0.7847 (m-30) cc_final: 0.7575 (m-30) REVERT: M 176 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7638 (tp30) REVERT: M 223 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8801 (m-10) REVERT: L 176 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7567 (tp30) REVERT: L 238 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8953 (pp) REVERT: K 238 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8926 (pp) REVERT: K 274 ASP cc_start: 0.8091 (m-30) cc_final: 0.7384 (m-30) REVERT: K 275 HIS cc_start: 0.7757 (m-70) cc_final: 0.7368 (m-70) REVERT: K 323 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7351 (mt-10) REVERT: J 238 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8863 (pp) REVERT: I 166 ASN cc_start: 0.8712 (t0) cc_final: 0.8326 (t0) REVERT: I 176 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7463 (tp30) REVERT: I 219 PHE cc_start: 0.8542 (p90) cc_final: 0.8225 (p90) REVERT: H 205 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7535 (mm-30) REVERT: H 206 ILE cc_start: 0.9326 (mt) cc_final: 0.9097 (mp) REVERT: H 238 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8997 (pp) REVERT: H 292 TYR cc_start: 0.8986 (p90) cc_final: 0.8687 (p90) REVERT: H 334 GLU cc_start: 0.7990 (tp30) cc_final: 0.7774 (tm-30) REVERT: G 166 ASN cc_start: 0.8721 (t0) cc_final: 0.8493 (t0) REVERT: G 223 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8829 (m-10) REVERT: G 238 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8989 (pp) REVERT: F 176 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7597 (tp30) REVERT: E 223 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: E 274 ASP cc_start: 0.8434 (m-30) cc_final: 0.8042 (m-30) REVERT: E 275 HIS cc_start: 0.7705 (m-70) cc_final: 0.7396 (m-70) REVERT: E 307 GLU cc_start: 0.6778 (tt0) cc_final: 0.6348 (tt0) REVERT: E 331 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7805 (mt0) REVERT: D 238 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8842 (pp) REVERT: D 245 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 166 ASN cc_start: 0.8756 (t0) cc_final: 0.8434 (t0) REVERT: C 176 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7491 (tp30) REVERT: C 205 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 238 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8935 (pp) REVERT: C 263 TYR cc_start: 0.9053 (p90) cc_final: 0.8632 (p90) REVERT: B 238 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8955 (pp) REVERT: A 176 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7793 (tp30) REVERT: A 328 TYR cc_start: 0.8895 (m-80) cc_final: 0.8401 (m-80) REVERT: W 238 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8974 (pp) REVERT: W 241 GLU cc_start: 0.7522 (mp0) cc_final: 0.7227 (mp0) REVERT: V 205 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: V 215 GLN cc_start: 0.8967 (tt0) cc_final: 0.8423 (tt0) REVERT: V 238 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8891 (pp) REVERT: V 275 HIS cc_start: 0.7724 (m-70) cc_final: 0.7342 (m-70) REVERT: U 223 TYR cc_start: 0.9013 (m-80) cc_final: 0.8782 (m-80) REVERT: U 238 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8889 (pp) REVERT: U 275 HIS cc_start: 0.7723 (m-70) cc_final: 0.7403 (m-70) REVERT: X 166 ASN cc_start: 0.8765 (t0) cc_final: 0.8521 (t0) REVERT: X 238 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9030 (pp) REVERT: X 334 GLU cc_start: 0.7565 (tp30) cc_final: 0.7266 (tp30) REVERT: a 89 MET cc_start: 0.7969 (mtp) cc_final: 0.7688 (mtp) REVERT: a 113 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8397 (ttp80) REVERT: a 194 TYR cc_start: 0.8856 (m-80) cc_final: 0.8563 (m-80) REVERT: b 176 ASP cc_start: 0.8309 (p0) cc_final: 0.7833 (p0) REVERT: c 189 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8634 (ttpp) REVERT: c 194 TYR cc_start: 0.8576 (m-80) cc_final: 0.8329 (m-80) REVERT: d 22 GLU cc_start: 0.7373 (mp0) cc_final: 0.6887 (mp0) REVERT: d 134 ASP cc_start: 0.6713 (m-30) cc_final: 0.6295 (m-30) REVERT: d 160 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7224 (mm-30) REVERT: f 48 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7528 (mmp-170) REVERT: f 176 ASP cc_start: 0.8054 (p0) cc_final: 0.7830 (p0) REVERT: g 112 GLN cc_start: 0.8842 (mt0) cc_final: 0.8335 (mt0) REVERT: g 171 LYS cc_start: 0.9332 (tptm) cc_final: 0.9088 (tptp) REVERT: g 176 ASP cc_start: 0.8083 (p0) cc_final: 0.7861 (p0) REVERT: g 194 TYR cc_start: 0.8542 (m-80) cc_final: 0.8173 (m-80) REVERT: h 107 TYR cc_start: 0.9203 (m-80) cc_final: 0.8936 (m-10) REVERT: h 112 GLN cc_start: 0.8746 (mt0) cc_final: 0.8335 (mt0) REVERT: h 176 ASP cc_start: 0.8073 (p0) cc_final: 0.7662 (p0) REVERT: i 26 SER cc_start: 0.9088 (p) cc_final: 0.8772 (t) REVERT: i 194 TYR cc_start: 0.8640 (m-80) cc_final: 0.8314 (m-80) REVERT: j 22 GLU cc_start: 0.7592 (mp0) cc_final: 0.7076 (mp0) REVERT: j 74 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7892 (ttp80) REVERT: j 191 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6980 (mm-30) REVERT: k 171 LYS cc_start: 0.9343 (tptp) cc_final: 0.9071 (tptp) REVERT: k 194 TYR cc_start: 0.8641 (m-80) cc_final: 0.8361 (m-80) REVERT: l 44 ASN cc_start: 0.9443 (t0) cc_final: 0.9126 (t0) REVERT: l 48 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7649 (mmt180) REVERT: l 103 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8756 (mtmt) REVERT: l 176 ASP cc_start: 0.7977 (p0) cc_final: 0.7675 (p0) REVERT: m 22 GLU cc_start: 0.7537 (mp0) cc_final: 0.7171 (mp0) REVERT: m 46 THR cc_start: 0.8936 (p) cc_final: 0.8590 (p) REVERT: m 113 ARG cc_start: 0.8634 (ttt180) cc_final: 0.8215 (ttt180) REVERT: m 176 ASP cc_start: 0.8274 (p0) cc_final: 0.8038 (p0) REVERT: m 194 TYR cc_start: 0.8702 (m-80) cc_final: 0.8280 (m-80) REVERT: n 107 TYR cc_start: 0.9197 (m-80) cc_final: 0.8958 (m-10) REVERT: n 112 GLN cc_start: 0.8828 (mt0) cc_final: 0.8494 (mt0) REVERT: n 176 ASP cc_start: 0.8065 (p0) cc_final: 0.7627 (p0) REVERT: o 189 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8636 (ttpp) REVERT: o 194 TYR cc_start: 0.8723 (m-80) cc_final: 0.8401 (m-80) REVERT: p 21 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7597 (mmt90) REVERT: p 22 GLU cc_start: 0.7349 (mp0) cc_final: 0.7070 (mp0) REVERT: q 113 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8535 (ttp80) REVERT: q 194 TYR cc_start: 0.8629 (m-80) cc_final: 0.8399 (m-80) REVERT: r 176 ASP cc_start: 0.8008 (p0) cc_final: 0.7777 (p0) REVERT: s 113 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8088 (ttt180) REVERT: t 89 MET cc_start: 0.8113 (mmm) cc_final: 0.7678 (mmt) REVERT: t 107 TYR cc_start: 0.9223 (m-80) cc_final: 0.8914 (m-10) REVERT: t 112 GLN cc_start: 0.8813 (mt0) cc_final: 0.8486 (mt0) REVERT: t 176 ASP cc_start: 0.8081 (p0) cc_final: 0.7666 (p0) REVERT: u 26 SER cc_start: 0.9052 (p) cc_final: 0.8809 (t) REVERT: u 113 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8326 (ttt180) REVERT: u 189 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8533 (ttpp) REVERT: u 194 TYR cc_start: 0.8457 (m-80) cc_final: 0.8248 (m-80) REVERT: v 128 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8786 (mmtm) REVERT: v 176 ASP cc_start: 0.8115 (p0) cc_final: 0.7873 (p0) REVERT: v 194 TYR cc_start: 0.8641 (m-80) cc_final: 0.8282 (m-80) REVERT: w 171 LYS cc_start: 0.9284 (tptm) cc_final: 0.9024 (tptp) REVERT: w 194 TYR cc_start: 0.8648 (m-80) cc_final: 0.8252 (m-80) REVERT: x 30 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8264 (mm-40) REVERT: x 44 ASN cc_start: 0.9439 (t0) cc_final: 0.8945 (t0) REVERT: x 74 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7943 (ttp80) REVERT: x 113 ARG cc_start: 0.8990 (mtp85) cc_final: 0.8700 (ttt90) outliers start: 229 outliers final: 152 residues processed: 2007 average time/residue: 0.7701 time to fit residues: 2518.2545 Evaluate side-chains 1858 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1683 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 307 GLU Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 294 GLU Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain Q residue 174 LEU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 248 THR Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 294 GLU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 307 GLU Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain E residue 223 TYR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 250 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain W residue 307 GLU Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 273 SER Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain V residue 307 GLU Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 338 LEU Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 155 SER Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 89 MET Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 41 GLU Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 23 GLU Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 41 GLU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 155 SER Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 41 GLU Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain x residue 41 GLU Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 3.9990 chunk 460 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 604 optimal weight: 3.9990 chunk 335 optimal weight: 0.6980 chunk 692 optimal weight: 1.9990 chunk 561 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 414 optimal weight: 1.9990 chunk 728 optimal weight: 1.9990 chunk 204 optimal weight: 0.0170 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 331 GLN Q 331 GLN P 318 ASN L 215 GLN K 166 ASN J 331 GLN G 275 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 GLN V 331 GLN U 318 ASN ** U 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN b 112 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 ASN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 GLN j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 GLN ** l 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN ** v 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 72024 Z= 0.369 Angle : 0.593 7.401 97224 Z= 0.313 Chirality : 0.046 0.148 11208 Planarity : 0.003 0.024 12456 Dihedral : 4.468 24.611 9600 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.41 % Allowed : 14.34 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8688 helix: 2.04 (0.09), residues: 3456 sheet: 0.62 (0.12), residues: 1824 loop : -2.30 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 183 HIS 0.006 0.001 HIS G 275 PHE 0.012 0.001 PHE M 285 TYR 0.020 0.001 TYR T 328 ARG 0.007 0.001 ARG S 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1945 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1670 time to evaluate : 6.575 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: S 238 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9076 (pp) REVERT: T 206 ILE cc_start: 0.9436 (mt) cc_final: 0.9118 (mt) REVERT: T 238 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9040 (pp) REVERT: R 176 GLU cc_start: 0.8222 (tp30) cc_final: 0.8006 (tp30) REVERT: R 238 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9004 (pp) REVERT: R 274 ASP cc_start: 0.8637 (m-30) cc_final: 0.8323 (m-30) REVERT: R 307 GLU cc_start: 0.7003 (tt0) cc_final: 0.6724 (tt0) REVERT: Q 205 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: Q 223 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: Q 238 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9008 (pp) REVERT: Q 275 HIS cc_start: 0.7911 (m-70) cc_final: 0.7576 (m-70) REVERT: P 238 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8952 (pp) REVERT: P 278 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8043 (mtp180) REVERT: O 166 ASN cc_start: 0.8733 (t0) cc_final: 0.8360 (t0) REVERT: O 238 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9091 (pp) REVERT: O 307 GLU cc_start: 0.6880 (tt0) cc_final: 0.6674 (tt0) REVERT: N 161 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8351 (ttp-170) REVERT: N 238 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9037 (pp) REVERT: N 294 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: M 176 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7763 (tp30) REVERT: M 223 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8872 (m-10) REVERT: M 238 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9056 (pp) REVERT: L 176 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7636 (tp30) REVERT: L 238 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9026 (pp) REVERT: K 238 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8998 (pp) REVERT: K 274 ASP cc_start: 0.8187 (m-30) cc_final: 0.7533 (m-30) REVERT: K 275 HIS cc_start: 0.7783 (m-70) cc_final: 0.7429 (m-70) REVERT: J 176 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7735 (tp30) REVERT: J 238 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8917 (pp) REVERT: J 278 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8023 (mtp180) REVERT: I 166 ASN cc_start: 0.8774 (t0) cc_final: 0.8483 (t0) REVERT: I 176 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7511 (tp30) REVERT: I 238 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9066 (pp) REVERT: H 238 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9097 (pp) REVERT: G 166 ASN cc_start: 0.8891 (t0) cc_final: 0.8644 (t0) REVERT: G 223 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: G 238 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9019 (pp) REVERT: F 161 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8476 (ttp-170) REVERT: F 238 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8986 (pp) REVERT: E 238 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9013 (pp) REVERT: E 274 ASP cc_start: 0.8437 (m-30) cc_final: 0.8225 (m-30) REVERT: E 275 HIS cc_start: 0.7754 (m-70) cc_final: 0.7382 (m-70) REVERT: E 307 GLU cc_start: 0.6674 (tt0) cc_final: 0.6399 (tt0) REVERT: D 238 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8900 (pp) REVERT: D 245 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8014 (p) REVERT: D 251 ASP cc_start: 0.7801 (m-30) cc_final: 0.7564 (m-30) REVERT: D 328 TYR cc_start: 0.9073 (m-80) cc_final: 0.8442 (m-80) REVERT: C 166 ASN cc_start: 0.8773 (t0) cc_final: 0.8539 (t0) REVERT: C 238 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9015 (pp) REVERT: B 238 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9050 (pp) REVERT: A 159 ASP cc_start: 0.6114 (t0) cc_final: 0.5841 (t0) REVERT: A 176 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7863 (tp30) REVERT: A 228 VAL cc_start: 0.9153 (t) cc_final: 0.8859 (m) REVERT: A 238 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9002 (pp) REVERT: W 238 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9026 (pp) REVERT: V 205 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8288 (mm-30) REVERT: V 238 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9029 (pp) REVERT: V 275 HIS cc_start: 0.7739 (m-70) cc_final: 0.7339 (m-70) REVERT: U 238 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8905 (pp) REVERT: U 275 HIS cc_start: 0.7761 (m-70) cc_final: 0.7461 (m-70) REVERT: X 166 ASN cc_start: 0.8788 (t0) cc_final: 0.8521 (t0) REVERT: X 238 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9047 (pp) REVERT: X 334 GLU cc_start: 0.7548 (tp30) cc_final: 0.7318 (tp30) REVERT: a 23 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: a 48 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7873 (mmp80) REVERT: a 89 MET cc_start: 0.8249 (mtp) cc_final: 0.8007 (mtp) REVERT: a 113 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8422 (mtp85) REVERT: a 194 TYR cc_start: 0.8874 (m-80) cc_final: 0.8604 (m-80) REVERT: b 176 ASP cc_start: 0.8325 (p0) cc_final: 0.7947 (p0) REVERT: b 194 TYR cc_start: 0.8570 (m-80) cc_final: 0.8141 (m-80) REVERT: c 189 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8738 (ttpp) REVERT: c 194 TYR cc_start: 0.8617 (m-80) cc_final: 0.8202 (m-80) REVERT: d 22 GLU cc_start: 0.7484 (mp0) cc_final: 0.7268 (mp0) REVERT: f 48 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7575 (mmp-170) REVERT: f 176 ASP cc_start: 0.8154 (p0) cc_final: 0.7889 (p0) REVERT: g 176 ASP cc_start: 0.8153 (p0) cc_final: 0.7932 (p0) REVERT: g 194 TYR cc_start: 0.8649 (m-80) cc_final: 0.8211 (m-80) REVERT: h 107 TYR cc_start: 0.9218 (m-80) cc_final: 0.8983 (m-10) REVERT: h 176 ASP cc_start: 0.8051 (p0) cc_final: 0.7694 (p0) REVERT: i 26 SER cc_start: 0.9079 (p) cc_final: 0.8790 (t) REVERT: i 194 TYR cc_start: 0.8773 (m-80) cc_final: 0.8394 (m-80) REVERT: j 134 ASP cc_start: 0.6932 (m-30) cc_final: 0.6543 (m-30) REVERT: k 171 LYS cc_start: 0.9360 (tptp) cc_final: 0.9117 (tptp) REVERT: k 194 TYR cc_start: 0.8668 (m-80) cc_final: 0.8419 (m-80) REVERT: l 103 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8800 (mtmt) REVERT: l 176 ASP cc_start: 0.7959 (p0) cc_final: 0.7613 (p0) REVERT: m 46 THR cc_start: 0.8953 (p) cc_final: 0.8610 (p) REVERT: m 113 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8379 (ttt180) REVERT: n 107 TYR cc_start: 0.9215 (m-80) cc_final: 0.8998 (m-10) REVERT: n 112 GLN cc_start: 0.8843 (mt0) cc_final: 0.8498 (mt0) REVERT: n 176 ASP cc_start: 0.8005 (p0) cc_final: 0.7656 (p0) REVERT: o 26 SER cc_start: 0.9126 (p) cc_final: 0.8842 (t) REVERT: o 189 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8767 (ttpp) REVERT: o 194 TYR cc_start: 0.8725 (m-80) cc_final: 0.8304 (m-80) REVERT: q 48 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7922 (mmp80) REVERT: q 113 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8334 (mtp85) REVERT: q 194 TYR cc_start: 0.8662 (m-80) cc_final: 0.8362 (m-80) REVERT: r 176 ASP cc_start: 0.8066 (p0) cc_final: 0.7818 (p0) REVERT: s 176 ASP cc_start: 0.8301 (p0) cc_final: 0.8099 (p0) REVERT: s 194 TYR cc_start: 0.8697 (m-80) cc_final: 0.8228 (m-80) REVERT: t 22 GLU cc_start: 0.7594 (mp0) cc_final: 0.7355 (mp0) REVERT: t 107 TYR cc_start: 0.9235 (m-80) cc_final: 0.8996 (m-10) REVERT: t 112 GLN cc_start: 0.8846 (mt0) cc_final: 0.8489 (mt0) REVERT: t 176 ASP cc_start: 0.8056 (p0) cc_final: 0.7680 (p0) REVERT: u 22 GLU cc_start: 0.7690 (mp0) cc_final: 0.7446 (mp0) REVERT: u 26 SER cc_start: 0.9093 (p) cc_final: 0.8838 (t) REVERT: u 189 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8703 (ttpp) REVERT: u 194 TYR cc_start: 0.8619 (m-80) cc_final: 0.8287 (m-80) REVERT: v 113 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8651 (ttt90) REVERT: v 128 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8795 (mmtm) REVERT: v 176 ASP cc_start: 0.8197 (p0) cc_final: 0.7829 (p0) REVERT: w 46 THR cc_start: 0.9154 (p) cc_final: 0.8876 (p) REVERT: w 74 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7851 (ttp80) REVERT: w 194 TYR cc_start: 0.8736 (m-80) cc_final: 0.8300 (m-80) REVERT: x 26 SER cc_start: 0.9266 (p) cc_final: 0.9033 (t) REVERT: x 30 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8358 (mm-40) REVERT: x 74 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8113 (ttp80) outliers start: 275 outliers final: 194 residues processed: 1855 average time/residue: 0.7626 time to fit residues: 2292.9660 Evaluate side-chains 1804 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1576 time to evaluate : 6.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 248 THR Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain Q residue 174 LEU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 248 THR Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 294 GLU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 251 ASP Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 247 ASP Chi-restraints excluded: chain U residue 248 THR Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain U residue 306 ARG Chi-restraints excluded: chain U residue 338 LEU Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 155 SER Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 41 GLU Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 89 MET Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 23 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 23 GLU Chi-restraints excluded: chain n residue 41 GLU Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 58 SER Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 155 SER Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 26 SER Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 41 GLU Chi-restraints excluded: chain t residue 85 ASP Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 149 VAL Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain u residue 193 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain x residue 41 GLU Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 0.7980 chunk 731 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 476 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 812 optimal weight: 1.9990 chunk 674 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 268 optimal weight: 0.5980 chunk 426 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 GLN R 331 GLN Q 169 GLN G 275 HIS E 331 GLN D 331 GLN C 318 ASN V 169 GLN V 331 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN b 88 GLN b 196 ASN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN h 196 ASN ** j 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 GLN ** l 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 GLN p 88 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 112 GLN ** v 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 72024 Z= 0.200 Angle : 0.521 8.221 97224 Z= 0.278 Chirality : 0.044 0.150 11208 Planarity : 0.003 0.030 12456 Dihedral : 4.241 24.375 9600 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.14 % Allowed : 15.43 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 8688 helix: 2.29 (0.09), residues: 3432 sheet: 0.98 (0.12), residues: 1776 loop : -2.20 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 183 HIS 0.004 0.001 HIS R 275 PHE 0.014 0.001 PHE J 219 TYR 0.019 0.001 TYR T 328 ARG 0.008 0.001 ARG L 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1711 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 159 ASP cc_start: 0.5278 (t0) cc_final: 0.5048 (t0) REVERT: S 238 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9069 (pp) REVERT: T 206 ILE cc_start: 0.9413 (mt) cc_final: 0.9061 (mt) REVERT: T 238 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8858 (pp) REVERT: R 238 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (pp) REVERT: R 307 GLU cc_start: 0.6978 (tt0) cc_final: 0.6729 (tt0) REVERT: R 340 ILE cc_start: 0.8224 (mm) cc_final: 0.7990 (mm) REVERT: Q 238 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8931 (pp) REVERT: Q 275 HIS cc_start: 0.7846 (m-70) cc_final: 0.7519 (m-70) REVERT: P 176 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7814 (tp30) REVERT: P 251 ASP cc_start: 0.7831 (m-30) cc_final: 0.7617 (m-30) REVERT: O 166 ASN cc_start: 0.8732 (t0) cc_final: 0.8374 (t0) REVERT: O 238 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8985 (pp) REVERT: O 334 GLU cc_start: 0.7650 (tp30) cc_final: 0.7224 (tp30) REVERT: N 238 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8909 (pp) REVERT: M 159 ASP cc_start: 0.5671 (t0) cc_final: 0.5394 (t0) REVERT: M 176 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7668 (tp30) REVERT: M 223 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8790 (m-10) REVERT: M 238 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8971 (pp) REVERT: K 176 GLU cc_start: 0.8064 (tp30) cc_final: 0.7748 (tp30) REVERT: K 238 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8925 (pp) REVERT: K 241 GLU cc_start: 0.7565 (mp0) cc_final: 0.7289 (mp0) REVERT: K 274 ASP cc_start: 0.8224 (m-30) cc_final: 0.7574 (m-30) REVERT: K 275 HIS cc_start: 0.7681 (m-70) cc_final: 0.7343 (m-70) REVERT: K 331 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7940 (mt0) REVERT: J 238 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8854 (pp) REVERT: I 166 ASN cc_start: 0.8693 (t0) cc_final: 0.8388 (t0) REVERT: I 176 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7496 (tp30) REVERT: I 238 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8970 (pp) REVERT: I 263 TYR cc_start: 0.9024 (p90) cc_final: 0.8736 (p90) REVERT: I 307 GLU cc_start: 0.6838 (tt0) cc_final: 0.6604 (tt0) REVERT: I 334 GLU cc_start: 0.7725 (tp30) cc_final: 0.7247 (tp30) REVERT: H 238 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8948 (pp) REVERT: G 166 ASN cc_start: 0.8784 (t0) cc_final: 0.8571 (t0) REVERT: G 223 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8812 (m-10) REVERT: G 238 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9027 (pp) REVERT: G 246 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7326 (mmmt) REVERT: G 307 GLU cc_start: 0.6566 (tt0) cc_final: 0.6323 (tt0) REVERT: F 176 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7604 (tp30) REVERT: F 238 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8944 (pp) REVERT: E 238 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8887 (pp) REVERT: E 275 HIS cc_start: 0.7691 (m-70) cc_final: 0.7319 (m-70) REVERT: E 307 GLU cc_start: 0.6687 (tt0) cc_final: 0.6420 (tt0) REVERT: D 238 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8814 (pp) REVERT: D 245 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7973 (p) REVERT: D 251 ASP cc_start: 0.7770 (m-30) cc_final: 0.7532 (m-30) REVERT: D 328 TYR cc_start: 0.8992 (m-80) cc_final: 0.8391 (m-80) REVERT: D 331 GLN cc_start: 0.7731 (mt0) cc_final: 0.7418 (mt0) REVERT: C 166 ASN cc_start: 0.8684 (t0) cc_final: 0.8459 (t0) REVERT: C 238 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8967 (pp) REVERT: C 334 GLU cc_start: 0.7635 (tp30) cc_final: 0.7204 (tp30) REVERT: B 238 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8909 (pp) REVERT: B 294 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: A 176 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7786 (tp30) REVERT: A 228 VAL cc_start: 0.9193 (t) cc_final: 0.8993 (m) REVERT: A 238 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8976 (pp) REVERT: A 307 GLU cc_start: 0.6678 (tt0) cc_final: 0.6414 (tt0) REVERT: A 328 TYR cc_start: 0.8859 (m-80) cc_final: 0.8348 (m-80) REVERT: W 238 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8963 (pp) REVERT: V 205 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: V 238 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (pp) REVERT: V 246 LYS cc_start: 0.8123 (mptt) cc_final: 0.7920 (mmmt) REVERT: V 275 HIS cc_start: 0.7648 (m-70) cc_final: 0.7255 (m-70) REVERT: U 176 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7654 (tp30) REVERT: U 275 HIS cc_start: 0.7688 (m-70) cc_final: 0.7394 (m-70) REVERT: X 166 ASN cc_start: 0.8738 (t0) cc_final: 0.8503 (t0) REVERT: X 238 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8997 (pp) REVERT: a 23 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: a 48 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7833 (mmp80) REVERT: a 89 MET cc_start: 0.8153 (mtp) cc_final: 0.7788 (mtp) REVERT: a 113 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8501 (ttp80) REVERT: b 176 ASP cc_start: 0.8321 (p0) cc_final: 0.7947 (p0) REVERT: b 194 TYR cc_start: 0.8479 (m-80) cc_final: 0.8107 (m-80) REVERT: c 189 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8640 (ttpp) REVERT: c 194 TYR cc_start: 0.8616 (m-80) cc_final: 0.8370 (m-80) REVERT: d 134 ASP cc_start: 0.6686 (m-30) cc_final: 0.6269 (m-30) REVERT: f 48 ARG cc_start: 0.7956 (mmt-90) cc_final: 0.7590 (mmp-170) REVERT: g 112 GLN cc_start: 0.8765 (mt0) cc_final: 0.8508 (mt0) REVERT: g 176 ASP cc_start: 0.8105 (p0) cc_final: 0.7882 (p0) REVERT: g 194 TYR cc_start: 0.8581 (m-80) cc_final: 0.8270 (m-80) REVERT: h 107 TYR cc_start: 0.9178 (m-80) cc_final: 0.8927 (m-10) REVERT: h 112 GLN cc_start: 0.8708 (mt0) cc_final: 0.8376 (mt0) REVERT: h 176 ASP cc_start: 0.8074 (p0) cc_final: 0.7732 (p0) REVERT: i 26 SER cc_start: 0.9109 (p) cc_final: 0.8810 (t) REVERT: i 194 TYR cc_start: 0.8651 (m-80) cc_final: 0.8417 (m-80) REVERT: j 22 GLU cc_start: 0.7625 (mp0) cc_final: 0.7223 (mp0) REVERT: j 74 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7897 (ttp80) REVERT: j 114 LEU cc_start: 0.9494 (mt) cc_final: 0.9211 (mt) REVERT: j 134 ASP cc_start: 0.6570 (m-30) cc_final: 0.6174 (m-30) REVERT: k 171 LYS cc_start: 0.9352 (tptp) cc_final: 0.9096 (tptp) REVERT: l 48 ARG cc_start: 0.7895 (mmp80) cc_final: 0.7617 (mmp-170) REVERT: l 103 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8750 (mtmt) REVERT: l 176 ASP cc_start: 0.7952 (p0) cc_final: 0.7694 (p0) REVERT: l 194 TYR cc_start: 0.8584 (m-80) cc_final: 0.8307 (m-80) REVERT: m 46 THR cc_start: 0.8958 (p) cc_final: 0.8647 (p) REVERT: m 113 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8355 (ttt180) REVERT: m 176 ASP cc_start: 0.8284 (p0) cc_final: 0.7986 (p0) REVERT: n 107 TYR cc_start: 0.9198 (m-80) cc_final: 0.8955 (m-10) REVERT: n 112 GLN cc_start: 0.8834 (mt0) cc_final: 0.8443 (mt0) REVERT: n 176 ASP cc_start: 0.8037 (p0) cc_final: 0.7635 (p0) REVERT: o 26 SER cc_start: 0.9121 (p) cc_final: 0.8886 (t) REVERT: o 145 MET cc_start: 0.8227 (tpp) cc_final: 0.8005 (tpp) REVERT: o 189 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8661 (ttpp) REVERT: o 194 TYR cc_start: 0.8727 (m-80) cc_final: 0.8506 (m-80) REVERT: q 113 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8482 (ttp80) REVERT: q 194 TYR cc_start: 0.8649 (m-80) cc_final: 0.8435 (m-80) REVERT: r 176 ASP cc_start: 0.8094 (p0) cc_final: 0.7848 (p0) REVERT: s 113 ARG cc_start: 0.8411 (ttt180) cc_final: 0.8185 (ttt180) REVERT: s 176 ASP cc_start: 0.8257 (p0) cc_final: 0.8047 (p0) REVERT: s 194 TYR cc_start: 0.8647 (m-80) cc_final: 0.8271 (m-80) REVERT: t 22 GLU cc_start: 0.7622 (mp0) cc_final: 0.7388 (mp0) REVERT: t 107 TYR cc_start: 0.9238 (m-80) cc_final: 0.8983 (m-10) REVERT: t 176 ASP cc_start: 0.8072 (p0) cc_final: 0.7730 (p0) REVERT: u 22 GLU cc_start: 0.7690 (mp0) cc_final: 0.7408 (mp0) REVERT: u 189 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8525 (ttpp) REVERT: u 194 TYR cc_start: 0.8556 (m-80) cc_final: 0.8283 (m-80) REVERT: v 128 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8776 (mmtm) REVERT: v 176 ASP cc_start: 0.8102 (p0) cc_final: 0.7779 (p0) REVERT: v 194 TYR cc_start: 0.8700 (m-80) cc_final: 0.8359 (m-80) REVERT: w 46 THR cc_start: 0.9097 (p) cc_final: 0.8836 (p) REVERT: w 74 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7966 (ttp80) REVERT: w 194 TYR cc_start: 0.8729 (m-80) cc_final: 0.8331 (m-80) REVERT: x 26 SER cc_start: 0.9205 (p) cc_final: 0.8919 (t) REVERT: x 30 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8248 (mm-40) REVERT: x 74 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8193 (ttp80) outliers start: 253 outliers final: 181 residues processed: 1877 average time/residue: 0.7770 time to fit residues: 2392.7039 Evaluate side-chains 1785 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1575 time to evaluate : 6.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 248 THR Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 170 CYS Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 338 LEU Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain Q residue 174 LEU Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 294 GLU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain N residue 331 GLN Chi-restraints excluded: chain N residue 338 LEU Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 307 GLU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 228 VAL Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 170 CYS Chi-restraints excluded: chain U residue 250 LEU Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain U residue 338 LEU Chi-restraints excluded: chain X residue 223 TYR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 193 VAL Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 89 MET Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 116 GLN Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 23 GLU Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain h residue 189 LYS Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 41 GLU Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 155 SER Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 149 VAL Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain u residue 193 VAL Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain x residue 25 ILE Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 463 optimal weight: 1.9990 chunk 593 optimal weight: 1.9990 chunk 459 optimal weight: 0.7980 chunk 684 optimal weight: 0.9990 chunk 453 optimal weight: 0.6980 chunk 809 optimal weight: 3.9990 chunk 506 optimal weight: 0.3980 chunk 493 optimal weight: 0.0970 chunk 373 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 331 GLN ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS D 210 GLN D 331 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN b 88 GLN b 196 ASN d 112 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 112 GLN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 172 ASN p 112 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 72024 Z= 0.189 Angle : 0.512 7.749 97224 Z= 0.273 Chirality : 0.044 0.199 11208 Planarity : 0.003 0.029 12456 Dihedral : 4.105 23.973 9600 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.98 % Allowed : 15.72 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 8688 helix: 2.40 (0.09), residues: 3432 sheet: 1.11 (0.12), residues: 1776 loop : -2.11 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.004 0.000 HIS P 275 PHE 0.009 0.001 PHE I 219 TYR 0.021 0.001 TYR B 328 ARG 0.007 0.001 ARG T 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1911 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1671 time to evaluate : 6.424 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: S 159 ASP cc_start: 0.5427 (t0) cc_final: 0.5102 (t0) REVERT: S 238 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9013 (pp) REVERT: T 205 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7608 (mm-30) REVERT: T 206 ILE cc_start: 0.9417 (mt) cc_final: 0.9059 (mt) REVERT: T 238 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8827 (pp) REVERT: T 334 GLU cc_start: 0.7524 (tp30) cc_final: 0.7013 (tp30) REVERT: R 176 GLU cc_start: 0.8164 (tp30) cc_final: 0.7912 (tp30) REVERT: R 238 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8881 (pp) REVERT: Q 166 ASN cc_start: 0.8780 (t0) cc_final: 0.8265 (t0) REVERT: Q 223 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8649 (m-10) REVERT: Q 275 HIS cc_start: 0.7811 (m-70) cc_final: 0.7575 (m-70) REVERT: P 176 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7615 (tp30) REVERT: O 166 ASN cc_start: 0.8706 (t0) cc_final: 0.8348 (t0) REVERT: O 176 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7322 (tp30) REVERT: O 205 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7386 (mm-30) REVERT: O 238 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8917 (pp) REVERT: O 263 TYR cc_start: 0.8818 (p90) cc_final: 0.8418 (p90) REVERT: O 307 GLU cc_start: 0.6660 (tt0) cc_final: 0.6457 (tt0) REVERT: O 334 GLU cc_start: 0.7661 (tp30) cc_final: 0.7231 (tp30) REVERT: N 205 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7860 (mm-30) REVERT: N 238 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8860 (pp) REVERT: N 294 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: N 334 GLU cc_start: 0.7532 (tp30) cc_final: 0.7051 (tp30) REVERT: M 223 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8803 (m-10) REVERT: L 238 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8882 (pp) REVERT: K 238 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8911 (pp) REVERT: K 274 ASP cc_start: 0.8162 (m-30) cc_final: 0.7586 (m-30) REVERT: K 275 HIS cc_start: 0.7644 (m-70) cc_final: 0.7285 (m-70) REVERT: K 323 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7382 (mt-10) REVERT: J 176 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7811 (tp30) REVERT: J 238 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8830 (pp) REVERT: J 263 TYR cc_start: 0.8788 (p90) cc_final: 0.8509 (p90) REVERT: I 166 ASN cc_start: 0.8699 (t0) cc_final: 0.8382 (t0) REVERT: I 176 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7498 (tp30) REVERT: I 238 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8924 (pp) REVERT: I 334 GLU cc_start: 0.7613 (tp30) cc_final: 0.7251 (tp30) REVERT: H 238 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8960 (pp) REVERT: G 166 ASN cc_start: 0.8705 (t0) cc_final: 0.8496 (t0) REVERT: G 223 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8803 (m-10) REVERT: G 238 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9002 (pp) REVERT: G 250 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8561 (mt) REVERT: F 238 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 275 HIS cc_start: 0.7643 (m-70) cc_final: 0.7288 (m-70) REVERT: E 307 GLU cc_start: 0.6683 (tt0) cc_final: 0.6423 (tt0) REVERT: D 238 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8796 (pp) REVERT: D 245 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7932 (p) REVERT: D 251 ASP cc_start: 0.7754 (m-30) cc_final: 0.7537 (m-30) REVERT: C 166 ASN cc_start: 0.8646 (t0) cc_final: 0.8406 (t0) REVERT: C 238 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8892 (pp) REVERT: C 334 GLU cc_start: 0.7659 (tp30) cc_final: 0.7226 (tp30) REVERT: B 238 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8869 (pp) REVERT: A 176 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7745 (tp30) REVERT: A 228 VAL cc_start: 0.9133 (t) cc_final: 0.8933 (m) REVERT: A 238 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8938 (pp) REVERT: A 307 GLU cc_start: 0.6774 (tt0) cc_final: 0.6482 (tt0) REVERT: A 328 TYR cc_start: 0.8853 (m-80) cc_final: 0.8369 (m-80) REVERT: W 238 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8887 (pp) REVERT: V 205 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: V 223 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: V 275 HIS cc_start: 0.7624 (m-70) cc_final: 0.7240 (m-70) REVERT: U 176 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7635 (tp30) REVERT: U 238 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8839 (pp) REVERT: U 263 TYR cc_start: 0.8812 (p90) cc_final: 0.8482 (p90) REVERT: U 275 HIS cc_start: 0.7707 (m-70) cc_final: 0.7406 (m-70) REVERT: X 166 ASN cc_start: 0.8716 (t0) cc_final: 0.8472 (t0) REVERT: X 238 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8966 (pp) REVERT: a 23 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: a 89 MET cc_start: 0.8076 (mtp) cc_final: 0.7800 (mtp) REVERT: a 113 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8494 (ttp80) REVERT: b 21 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7660 (mmt90) REVERT: b 160 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7016 (mm-30) REVERT: b 176 ASP cc_start: 0.8295 (p0) cc_final: 0.7938 (p0) REVERT: b 194 TYR cc_start: 0.8507 (m-80) cc_final: 0.8159 (m-80) REVERT: c 189 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8592 (ttpp) REVERT: c 194 TYR cc_start: 0.8678 (m-80) cc_final: 0.8387 (m-80) REVERT: d 22 GLU cc_start: 0.7419 (mp0) cc_final: 0.7144 (mp0) REVERT: d 134 ASP cc_start: 0.6674 (m-30) cc_final: 0.6288 (m-30) REVERT: f 44 ASN cc_start: 0.9415 (t0) cc_final: 0.9003 (t0) REVERT: f 48 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7568 (mmp-170) REVERT: f 176 ASP cc_start: 0.8048 (p0) cc_final: 0.7786 (p0) REVERT: g 112 GLN cc_start: 0.8787 (mt0) cc_final: 0.8529 (mt0) REVERT: g 176 ASP cc_start: 0.8082 (p0) cc_final: 0.7822 (p0) REVERT: g 194 TYR cc_start: 0.8671 (m-80) cc_final: 0.8339 (m-80) REVERT: h 107 TYR cc_start: 0.9193 (m-80) cc_final: 0.8948 (m-10) REVERT: i 26 SER cc_start: 0.9110 (p) cc_final: 0.8801 (t) REVERT: i 194 TYR cc_start: 0.8688 (m-80) cc_final: 0.8436 (m-80) REVERT: j 74 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7923 (ttp80) REVERT: j 114 LEU cc_start: 0.9494 (mt) cc_final: 0.9244 (mt) REVERT: l 44 ASN cc_start: 0.9501 (t0) cc_final: 0.9162 (t0) REVERT: l 48 ARG cc_start: 0.7847 (mmp80) cc_final: 0.7610 (mmp-170) REVERT: l 103 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8757 (mtmt) REVERT: l 176 ASP cc_start: 0.7915 (p0) cc_final: 0.7683 (p0) REVERT: l 194 TYR cc_start: 0.8563 (m-80) cc_final: 0.8249 (m-80) REVERT: m 46 THR cc_start: 0.8979 (p) cc_final: 0.8708 (p) REVERT: m 113 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8380 (ttt180) REVERT: n 107 TYR cc_start: 0.9193 (m-80) cc_final: 0.8916 (m-10) REVERT: n 112 GLN cc_start: 0.8845 (mt0) cc_final: 0.8430 (mt0) REVERT: n 176 ASP cc_start: 0.8054 (p0) cc_final: 0.7646 (p0) REVERT: o 145 MET cc_start: 0.8237 (tpp) cc_final: 0.7995 (tpp) REVERT: o 189 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8614 (ttpp) REVERT: o 194 TYR cc_start: 0.8827 (m-80) cc_final: 0.8499 (m-80) REVERT: q 113 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8609 (ttp80) REVERT: q 194 TYR cc_start: 0.8690 (m-80) cc_final: 0.8475 (m-80) REVERT: r 176 ASP cc_start: 0.8079 (p0) cc_final: 0.7819 (p0) REVERT: r 194 TYR cc_start: 0.8448 (m-80) cc_final: 0.8166 (m-80) REVERT: s 176 ASP cc_start: 0.8283 (p0) cc_final: 0.8042 (p0) REVERT: t 107 TYR cc_start: 0.9239 (m-80) cc_final: 0.8952 (m-10) REVERT: t 176 ASP cc_start: 0.8081 (p0) cc_final: 0.7741 (p0) REVERT: u 189 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8607 (ttpp) REVERT: v 128 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8776 (mmtm) REVERT: v 176 ASP cc_start: 0.8088 (p0) cc_final: 0.7829 (p0) REVERT: v 194 TYR cc_start: 0.8653 (m-80) cc_final: 0.8282 (m-80) REVERT: w 46 THR cc_start: 0.9086 (p) cc_final: 0.8820 (p) REVERT: w 194 TYR cc_start: 0.8728 (m-80) cc_final: 0.8328 (m-80) REVERT: x 26 SER cc_start: 0.9238 (p) cc_final: 0.8932 (t) REVERT: x 30 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8225 (mm-40) outliers start: 240 outliers final: 177 residues processed: 1831 average time/residue: 0.7257 time to fit residues: 2171.6336 Evaluate side-chains 1796 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1589 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 248 THR Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 338 LEU Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 247 ASP Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 294 GLU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain N residue 331 GLN Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain M residue 307 GLU Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 251 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain W residue 307 GLU Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 223 TYR Chi-restraints excluded: chain V residue 228 VAL Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 170 CYS Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain X residue 223 TYR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 193 VAL Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 116 GLN Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 23 GLU Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain h residue 189 LYS Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 143 LYS Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain u residue 193 VAL Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain x residue 25 ILE Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 61 VAL Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 483 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 514 optimal weight: 0.9980 chunk 551 optimal weight: 0.4980 chunk 400 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 636 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 GLN R 331 GLN Q 169 GLN P 275 HIS K 331 GLN G 275 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 GLN ** U 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN ** j 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN p 112 GLN r 172 ASN t 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 72024 Z= 0.315 Angle : 0.586 9.503 97224 Z= 0.309 Chirality : 0.046 0.216 11208 Planarity : 0.003 0.025 12456 Dihedral : 4.301 24.329 9600 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.31 % Allowed : 15.58 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8688 helix: 2.26 (0.09), residues: 3456 sheet: 0.82 (0.12), residues: 1824 loop : -2.08 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 183 HIS 0.004 0.001 HIS P 275 PHE 0.014 0.001 PHE R 219 TYR 0.022 0.001 TYR N 328 ARG 0.008 0.001 ARG X 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1900 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1633 time to evaluate : 6.387 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: S 159 ASP cc_start: 0.5742 (t0) cc_final: 0.5529 (t0) REVERT: S 238 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9067 (pp) REVERT: T 206 ILE cc_start: 0.9457 (mt) cc_final: 0.9104 (mt) REVERT: T 238 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8956 (pp) REVERT: T 334 GLU cc_start: 0.7526 (tp30) cc_final: 0.7001 (tp30) REVERT: R 238 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8948 (pp) REVERT: Q 223 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: Q 238 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8919 (pp) REVERT: P 176 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7862 (tp30) REVERT: P 238 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8907 (pp) REVERT: O 166 ASN cc_start: 0.8751 (t0) cc_final: 0.8416 (t0) REVERT: O 238 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9043 (pp) REVERT: O 334 GLU cc_start: 0.7688 (tp30) cc_final: 0.7245 (tp30) REVERT: N 238 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8991 (pp) REVERT: M 223 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8814 (m-10) REVERT: M 238 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9025 (pp) REVERT: L 176 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7663 (tp30) REVERT: L 238 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8958 (pp) REVERT: K 238 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8927 (pp) REVERT: K 274 ASP cc_start: 0.8176 (m-30) cc_final: 0.7633 (m-30) REVERT: K 275 HIS cc_start: 0.7711 (m-70) cc_final: 0.7346 (m-70) REVERT: J 176 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7892 (tp30) REVERT: J 238 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8890 (pp) REVERT: J 278 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7991 (mtp180) REVERT: I 166 ASN cc_start: 0.8729 (t0) cc_final: 0.8444 (t0) REVERT: I 176 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7522 (tp30) REVERT: I 238 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9048 (pp) REVERT: I 307 GLU cc_start: 0.6767 (tt0) cc_final: 0.6521 (tt0) REVERT: I 334 GLU cc_start: 0.7630 (tp30) cc_final: 0.7283 (tp30) REVERT: H 238 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8966 (pp) REVERT: H 328 TYR cc_start: 0.8941 (m-80) cc_final: 0.8718 (m-80) REVERT: G 166 ASN cc_start: 0.8863 (t0) cc_final: 0.8655 (t0) REVERT: G 223 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8863 (m-10) REVERT: G 238 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9049 (pp) REVERT: G 250 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8670 (mt) REVERT: F 176 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7655 (tp30) REVERT: F 238 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8933 (pp) REVERT: E 238 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8896 (pp) REVERT: E 275 HIS cc_start: 0.7670 (m-70) cc_final: 0.7293 (m-70) REVERT: E 308 GLU cc_start: 0.5910 (mm-30) cc_final: 0.5576 (tp30) REVERT: D 153 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8039 (mm) REVERT: D 238 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8827 (pp) REVERT: D 245 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7953 (p) REVERT: D 251 ASP cc_start: 0.7828 (m-30) cc_final: 0.7577 (m-30) REVERT: D 328 TYR cc_start: 0.9083 (m-80) cc_final: 0.8757 (m-80) REVERT: C 166 ASN cc_start: 0.8755 (t0) cc_final: 0.8505 (t0) REVERT: C 238 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9012 (pp) REVERT: C 334 GLU cc_start: 0.7677 (tp30) cc_final: 0.7232 (tp30) REVERT: B 238 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9039 (pp) REVERT: B 294 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 176 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7779 (tp30) REVERT: A 238 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9022 (pp) REVERT: A 307 GLU cc_start: 0.6717 (tt0) cc_final: 0.6434 (tt0) REVERT: W 238 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8983 (pp) REVERT: V 205 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: V 223 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: V 238 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8906 (pp) REVERT: V 275 HIS cc_start: 0.7722 (m-70) cc_final: 0.7320 (m-70) REVERT: U 176 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7946 (tp30) REVERT: U 238 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8866 (pp) REVERT: U 275 HIS cc_start: 0.7737 (m-70) cc_final: 0.7422 (m-70) REVERT: U 307 GLU cc_start: 0.6989 (tt0) cc_final: 0.6652 (tt0) REVERT: X 166 ASN cc_start: 0.8801 (t0) cc_final: 0.8539 (t0) REVERT: X 238 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9032 (pp) REVERT: a 23 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: a 89 MET cc_start: 0.8088 (mtp) cc_final: 0.7817 (mtp) REVERT: a 113 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8362 (mtp85) REVERT: a 194 TYR cc_start: 0.8708 (m-80) cc_final: 0.8464 (m-80) REVERT: b 21 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7725 (mmt90) REVERT: b 160 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6988 (mm-30) REVERT: b 176 ASP cc_start: 0.8354 (p0) cc_final: 0.7987 (p0) REVERT: b 194 TYR cc_start: 0.8519 (m-80) cc_final: 0.8114 (m-80) REVERT: c 194 TYR cc_start: 0.8734 (m-80) cc_final: 0.8415 (m-80) REVERT: f 48 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7559 (mmp-170) REVERT: f 176 ASP cc_start: 0.8191 (p0) cc_final: 0.7899 (p0) REVERT: g 176 ASP cc_start: 0.8172 (p0) cc_final: 0.7917 (p0) REVERT: g 194 TYR cc_start: 0.8704 (m-80) cc_final: 0.8325 (m-80) REVERT: h 194 TYR cc_start: 0.8379 (m-80) cc_final: 0.8019 (m-80) REVERT: i 26 SER cc_start: 0.9084 (p) cc_final: 0.8808 (t) REVERT: i 194 TYR cc_start: 0.8743 (m-80) cc_final: 0.8385 (m-80) REVERT: j 22 GLU cc_start: 0.7638 (mp0) cc_final: 0.7438 (mp0) REVERT: j 74 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7829 (ttp80) REVERT: j 134 ASP cc_start: 0.6945 (m-30) cc_final: 0.6529 (m-30) REVERT: l 103 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8795 (mtmt) REVERT: l 176 ASP cc_start: 0.8003 (p0) cc_final: 0.7746 (p0) REVERT: m 46 THR cc_start: 0.8975 (p) cc_final: 0.8679 (p) REVERT: m 113 ARG cc_start: 0.8723 (ttt180) cc_final: 0.8343 (ttt180) REVERT: n 107 TYR cc_start: 0.9202 (m-80) cc_final: 0.8955 (m-10) REVERT: n 112 GLN cc_start: 0.8862 (mt0) cc_final: 0.8471 (mt0) REVERT: n 176 ASP cc_start: 0.8094 (p0) cc_final: 0.7740 (p0) REVERT: o 194 TYR cc_start: 0.8791 (m-80) cc_final: 0.8446 (m-80) REVERT: q 113 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8364 (ttp80) REVERT: q 194 TYR cc_start: 0.8666 (m-80) cc_final: 0.8407 (m-80) REVERT: r 176 ASP cc_start: 0.8157 (p0) cc_final: 0.7853 (p0) REVERT: s 74 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8052 (ttp80) REVERT: s 176 ASP cc_start: 0.8295 (p0) cc_final: 0.8095 (p0) REVERT: t 107 TYR cc_start: 0.9199 (m-80) cc_final: 0.8974 (m-10) REVERT: t 176 ASP cc_start: 0.8136 (p0) cc_final: 0.7764 (p0) REVERT: u 26 SER cc_start: 0.9178 (p) cc_final: 0.8911 (t) REVERT: v 128 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8793 (mmtm) REVERT: v 176 ASP cc_start: 0.8153 (p0) cc_final: 0.7893 (p0) REVERT: w 46 THR cc_start: 0.9058 (p) cc_final: 0.8767 (p) REVERT: w 74 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8124 (ttp80) REVERT: w 194 TYR cc_start: 0.8735 (m-80) cc_final: 0.8306 (m-80) REVERT: x 26 SER cc_start: 0.9245 (p) cc_final: 0.8940 (t) REVERT: x 30 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8380 (mm-40) REVERT: x 112 GLN cc_start: 0.8741 (mt0) cc_final: 0.8396 (mt0) outliers start: 267 outliers final: 210 residues processed: 1811 average time/residue: 0.7491 time to fit residues: 2213.5293 Evaluate side-chains 1815 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1569 time to evaluate : 6.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 248 THR Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 338 LEU Chi-restraints excluded: chain R residue 223 TYR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 251 ASP Chi-restraints excluded: chain R residue 307 GLU Chi-restraints excluded: chain Q residue 169 GLN Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 247 ASP Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 294 GLU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain N residue 331 GLN Chi-restraints excluded: chain N residue 338 LEU Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain J residue 338 LEU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 251 ASP Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain W residue 307 GLU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 223 TYR Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 273 SER Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 170 CYS Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 247 ASP Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain U residue 306 ARG Chi-restraints excluded: chain X residue 223 TYR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 193 VAL Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 116 GLN Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 85 ASP Chi-restraints excluded: chain g residue 97 SER Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 61 VAL Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 85 ASP Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 155 SER Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 155 SER Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 58 SER Chi-restraints excluded: chain t residue 143 LYS Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain u residue 193 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain x residue 25 ILE Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 1.9990 chunk 775 optimal weight: 0.9990 chunk 707 optimal weight: 0.5980 chunk 754 optimal weight: 0.8980 chunk 454 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 592 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 681 optimal weight: 0.9990 chunk 713 optimal weight: 0.5980 chunk 751 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 331 GLN Q 169 GLN K 169 GLN I 275 HIS G 275 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 GLN U 210 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN b 196 ASN e 196 ASN h 196 ASN ** j 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 GLN n 196 ASN p 88 GLN p 112 GLN t 88 GLN t 196 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 72024 Z= 0.236 Angle : 0.560 9.188 97224 Z= 0.297 Chirality : 0.045 0.195 11208 Planarity : 0.003 0.054 12456 Dihedral : 4.209 24.198 9600 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.20 % Allowed : 15.94 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8688 helix: 2.33 (0.09), residues: 3456 sheet: 0.11 (0.11), residues: 2184 loop : -1.92 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.003 0.001 HIS I 275 PHE 0.017 0.001 PHE R 219 TYR 0.021 0.001 TYR N 328 ARG 0.009 0.001 ARG I 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1897 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1639 time to evaluate : 6.393 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: S 238 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9063 (pp) REVERT: T 206 ILE cc_start: 0.9447 (mt) cc_final: 0.9077 (mt) REVERT: T 238 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8869 (pp) REVERT: T 334 GLU cc_start: 0.7510 (tp30) cc_final: 0.7019 (tp30) REVERT: R 238 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8914 (pp) REVERT: R 340 ILE cc_start: 0.7624 (mm) cc_final: 0.7415 (mm) REVERT: Q 223 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8663 (m-10) REVERT: Q 238 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8870 (pp) REVERT: P 238 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8854 (pp) REVERT: O 166 ASN cc_start: 0.8789 (t0) cc_final: 0.8432 (t0) REVERT: O 238 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8991 (pp) REVERT: O 334 GLU cc_start: 0.7651 (tp30) cc_final: 0.7236 (tp30) REVERT: N 238 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8889 (pp) REVERT: N 334 GLU cc_start: 0.7568 (tp30) cc_final: 0.7029 (tp30) REVERT: M 223 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8765 (m-10) REVERT: M 238 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9004 (pp) REVERT: L 176 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7634 (tp30) REVERT: L 238 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8890 (pp) REVERT: K 238 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8893 (pp) REVERT: K 274 ASP cc_start: 0.8167 (m-30) cc_final: 0.7666 (m-30) REVERT: K 275 HIS cc_start: 0.7673 (m-70) cc_final: 0.7315 (m-70) REVERT: J 176 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7860 (tp30) REVERT: J 238 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8871 (pp) REVERT: I 166 ASN cc_start: 0.8732 (t0) cc_final: 0.8429 (t0) REVERT: I 238 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8967 (pp) REVERT: I 334 GLU cc_start: 0.7625 (tp30) cc_final: 0.7297 (tp30) REVERT: H 238 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8945 (pp) REVERT: H 328 TYR cc_start: 0.8853 (m-80) cc_final: 0.8638 (m-80) REVERT: G 166 ASN cc_start: 0.8824 (t0) cc_final: 0.8624 (t0) REVERT: G 223 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8827 (m-10) REVERT: G 238 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9025 (pp) REVERT: G 250 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8610 (mt) REVERT: F 176 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7641 (tp30) REVERT: F 238 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8851 (pp) REVERT: E 238 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8850 (pp) REVERT: E 275 HIS cc_start: 0.7651 (m-70) cc_final: 0.7252 (m-70) REVERT: E 308 GLU cc_start: 0.5898 (mm-30) cc_final: 0.5434 (tp30) REVERT: D 210 GLN cc_start: 0.8542 (tp40) cc_final: 0.8231 (tt0) REVERT: D 238 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8792 (pp) REVERT: D 245 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7942 (p) REVERT: D 251 ASP cc_start: 0.7769 (m-30) cc_final: 0.7568 (m-30) REVERT: D 328 TYR cc_start: 0.9021 (m-80) cc_final: 0.8638 (m-80) REVERT: C 166 ASN cc_start: 0.8726 (t0) cc_final: 0.8503 (t0) REVERT: C 238 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8972 (pp) REVERT: B 238 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8926 (pp) REVERT: A 176 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7744 (tp30) REVERT: A 228 VAL cc_start: 0.9123 (t) cc_final: 0.8914 (m) REVERT: A 238 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8983 (pp) REVERT: A 307 GLU cc_start: 0.6751 (tt0) cc_final: 0.6509 (tt0) REVERT: A 328 TYR cc_start: 0.8858 (m-80) cc_final: 0.8403 (m-80) REVERT: W 238 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8916 (pp) REVERT: V 205 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: V 223 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8571 (m-10) REVERT: V 238 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8852 (pp) REVERT: V 260 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7991 (tm-30) REVERT: V 275 HIS cc_start: 0.7654 (m-70) cc_final: 0.7265 (m-70) REVERT: U 176 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7705 (tp30) REVERT: U 238 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8840 (pp) REVERT: U 275 HIS cc_start: 0.7729 (m-70) cc_final: 0.7419 (m-70) REVERT: U 307 GLU cc_start: 0.6657 (tt0) cc_final: 0.6393 (tt0) REVERT: X 166 ASN cc_start: 0.8782 (t0) cc_final: 0.8567 (t0) REVERT: X 238 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8997 (pp) REVERT: a 23 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: a 89 MET cc_start: 0.8061 (mtp) cc_final: 0.7710 (mtp) REVERT: a 113 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8457 (ttp80) REVERT: a 194 TYR cc_start: 0.8689 (m-80) cc_final: 0.8467 (m-80) REVERT: b 21 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7592 (mmt90) REVERT: b 160 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7031 (mm-30) REVERT: b 176 ASP cc_start: 0.8325 (p0) cc_final: 0.7959 (p0) REVERT: b 194 TYR cc_start: 0.8541 (m-80) cc_final: 0.8154 (m-80) REVERT: c 194 TYR cc_start: 0.8712 (m-80) cc_final: 0.8428 (m-80) REVERT: d 22 GLU cc_start: 0.7587 (mp0) cc_final: 0.7279 (mp0) REVERT: d 112 GLN cc_start: 0.8690 (mt0) cc_final: 0.8326 (mt0) REVERT: f 44 ASN cc_start: 0.9435 (t0) cc_final: 0.9119 (t0) REVERT: f 48 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7541 (mmp-170) REVERT: f 176 ASP cc_start: 0.8147 (p0) cc_final: 0.7828 (p0) REVERT: g 176 ASP cc_start: 0.8109 (p0) cc_final: 0.7844 (p0) REVERT: g 194 TYR cc_start: 0.8670 (m-80) cc_final: 0.8352 (m-80) REVERT: i 26 SER cc_start: 0.9084 (p) cc_final: 0.8816 (t) REVERT: i 194 TYR cc_start: 0.8712 (m-80) cc_final: 0.8421 (m-80) REVERT: j 22 GLU cc_start: 0.7622 (mp0) cc_final: 0.7402 (mp0) REVERT: j 74 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7893 (ttp80) REVERT: j 134 ASP cc_start: 0.6578 (m-30) cc_final: 0.6157 (m-30) REVERT: l 44 ASN cc_start: 0.9462 (t0) cc_final: 0.9165 (t0) REVERT: l 48 ARG cc_start: 0.7817 (mmp80) cc_final: 0.7596 (mmp-170) REVERT: l 103 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8763 (mtmt) REVERT: l 176 ASP cc_start: 0.7949 (p0) cc_final: 0.7719 (p0) REVERT: m 22 GLU cc_start: 0.7666 (mp0) cc_final: 0.7413 (mp0) REVERT: m 46 THR cc_start: 0.8936 (p) cc_final: 0.8634 (p) REVERT: m 113 ARG cc_start: 0.8629 (ttt180) cc_final: 0.8388 (ttt180) REVERT: n 107 TYR cc_start: 0.9198 (m-80) cc_final: 0.8938 (m-10) REVERT: n 112 GLN cc_start: 0.8870 (mt0) cc_final: 0.8459 (mt0) REVERT: n 176 ASP cc_start: 0.8062 (p0) cc_final: 0.7716 (p0) REVERT: o 194 TYR cc_start: 0.8791 (m-80) cc_final: 0.8517 (m-80) REVERT: q 113 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8548 (ttp80) REVERT: q 194 TYR cc_start: 0.8683 (m-80) cc_final: 0.8451 (m-80) REVERT: r 176 ASP cc_start: 0.8111 (p0) cc_final: 0.7836 (p0) REVERT: s 74 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8017 (ttp80) REVERT: s 176 ASP cc_start: 0.8296 (p0) cc_final: 0.8096 (p0) REVERT: t 107 TYR cc_start: 0.9180 (m-80) cc_final: 0.8949 (m-10) REVERT: t 176 ASP cc_start: 0.8103 (p0) cc_final: 0.7740 (p0) REVERT: u 26 SER cc_start: 0.9163 (p) cc_final: 0.8902 (t) REVERT: v 128 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8785 (mmtm) REVERT: v 176 ASP cc_start: 0.8131 (p0) cc_final: 0.7870 (p0) REVERT: w 46 THR cc_start: 0.9006 (p) cc_final: 0.8724 (p) REVERT: w 74 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8084 (ttp80) REVERT: w 194 TYR cc_start: 0.8710 (m-80) cc_final: 0.8296 (m-80) REVERT: x 26 SER cc_start: 0.9246 (p) cc_final: 0.8910 (t) REVERT: x 30 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8256 (mm-40) outliers start: 258 outliers final: 205 residues processed: 1811 average time/residue: 0.7274 time to fit residues: 2162.2918 Evaluate side-chains 1840 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1601 time to evaluate : 6.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 248 THR Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 338 LEU Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 307 GLU Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain Q residue 169 GLN Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain P residue 170 CYS Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 250 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain N residue 331 GLN Chi-restraints excluded: chain N residue 338 LEU Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 307 GLU Chi-restraints excluded: chain K residue 169 GLN Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 223 TYR Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain W residue 307 GLU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 205 GLU Chi-restraints excluded: chain V residue 223 TYR Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain V residue 338 LEU Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 170 CYS Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 248 THR Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain U residue 306 ARG Chi-restraints excluded: chain U residue 338 LEU Chi-restraints excluded: chain X residue 223 TYR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 334 GLU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 108 SER Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 193 VAL Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 116 GLN Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 23 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 132 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 61 VAL Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 116 GLN Chi-restraints excluded: chain n residue 155 SER Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 149 VAL Chi-restraints excluded: chain s residue 155 SER Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain v residue 183 SER Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain w residue 163 VAL Chi-restraints excluded: chain w residue 186 LEU Chi-restraints excluded: chain x residue 25 ILE Chi-restraints excluded: chain x residue 58 SER Chi-restraints excluded: chain x residue 108 SER Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 0.7980 chunk 797 optimal weight: 0.6980 chunk 486 optimal weight: 0.6980 chunk 378 optimal weight: 0.9990 chunk 554 optimal weight: 0.7980 chunk 836 optimal weight: 0.0170 chunk 770 optimal weight: 0.0170 chunk 666 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 514 optimal weight: 0.9980 chunk 408 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 318 ASN T 210 GLN R 210 GLN R 318 ASN R 331 GLN G 275 HIS E 210 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 210 GLN U 210 GLN ** a 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN b 196 ASN h 112 GLN h 196 ASN ** j 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN ** k 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 GLN p 60 GLN p 88 GLN p 112 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 88 GLN t 112 GLN t 196 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 72024 Z= 0.187 Angle : 0.550 9.514 97224 Z= 0.292 Chirality : 0.044 0.183 11208 Planarity : 0.003 0.038 12456 Dihedral : 4.092 23.755 9600 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.74 % Allowed : 16.54 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 8688 helix: 2.43 (0.09), residues: 3456 sheet: 0.21 (0.11), residues: 2184 loop : -1.88 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 183 HIS 0.004 0.000 HIS Q 275 PHE 0.010 0.001 PHE E 219 TYR 0.020 0.001 TYR h 194 ARG 0.008 0.001 ARG T 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1674 time to evaluate : 6.451 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: S 205 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7614 (mm-30) REVERT: S 238 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9005 (pp) REVERT: S 328 TYR cc_start: 0.8880 (m-80) cc_final: 0.8388 (m-80) REVERT: T 206 ILE cc_start: 0.9435 (mt) cc_final: 0.9055 (mt) REVERT: T 238 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8843 (pp) REVERT: T 334 GLU cc_start: 0.7491 (tp30) cc_final: 0.7109 (tp30) REVERT: R 238 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8806 (pp) REVERT: R 274 ASP cc_start: 0.8751 (m-30) cc_final: 0.8537 (m-30) REVERT: Q 223 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: Q 238 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8844 (pp) REVERT: P 238 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8837 (pp) REVERT: P 263 TYR cc_start: 0.8804 (p90) cc_final: 0.8561 (p90) REVERT: P 307 GLU cc_start: 0.6813 (tt0) cc_final: 0.6546 (tt0) REVERT: O 166 ASN cc_start: 0.8761 (t0) cc_final: 0.8423 (t0) REVERT: O 238 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8893 (pp) REVERT: O 275 HIS cc_start: 0.7559 (m-70) cc_final: 0.7337 (m-70) REVERT: O 334 GLU cc_start: 0.7647 (tp30) cc_final: 0.7242 (tp30) REVERT: N 238 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8835 (pp) REVERT: N 334 GLU cc_start: 0.7542 (tp30) cc_final: 0.7066 (tp30) REVERT: M 223 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8751 (m-10) REVERT: M 238 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8937 (pp) REVERT: L 176 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7570 (tp30) REVERT: L 238 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8833 (pp) REVERT: K 238 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8883 (pp) REVERT: K 274 ASP cc_start: 0.8128 (m-30) cc_final: 0.7621 (m-30) REVERT: K 275 HIS cc_start: 0.7644 (m-70) cc_final: 0.7260 (m-70) REVERT: K 323 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7386 (mt-10) REVERT: J 176 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7811 (tp30) REVERT: J 238 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8831 (pp) REVERT: J 263 TYR cc_start: 0.8722 (p90) cc_final: 0.8453 (p90) REVERT: I 166 ASN cc_start: 0.8646 (t0) cc_final: 0.8353 (t0) REVERT: I 238 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8864 (pp) REVERT: I 334 GLU cc_start: 0.7621 (tp30) cc_final: 0.7312 (tp30) REVERT: H 238 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8904 (pp) REVERT: H 328 TYR cc_start: 0.8820 (m-80) cc_final: 0.8583 (m-80) REVERT: G 223 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8787 (m-10) REVERT: G 250 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 176 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7590 (tp30) REVERT: F 238 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8697 (pp) REVERT: E 238 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8781 (pp) REVERT: E 275 HIS cc_start: 0.7601 (m-70) cc_final: 0.7187 (m-70) REVERT: E 308 GLU cc_start: 0.5825 (mm-30) cc_final: 0.5429 (tp30) REVERT: D 153 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7987 (mm) REVERT: D 210 GLN cc_start: 0.8442 (tp40) cc_final: 0.8218 (tt0) REVERT: D 238 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8771 (pp) REVERT: D 245 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 166 ASN cc_start: 0.8704 (t0) cc_final: 0.8503 (t0) REVERT: C 205 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 238 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8869 (pp) REVERT: C 334 GLU cc_start: 0.7653 (tp30) cc_final: 0.7247 (tp30) REVERT: B 238 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8842 (pp) REVERT: B 294 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 161 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8492 (ttp-170) REVERT: A 238 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8955 (pp) REVERT: A 328 TYR cc_start: 0.8790 (m-80) cc_final: 0.8363 (m-80) REVERT: W 238 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8837 (pp) REVERT: V 223 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8663 (m-10) REVERT: V 238 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8772 (pp) REVERT: V 275 HIS cc_start: 0.7579 (m-70) cc_final: 0.7222 (m-70) REVERT: U 238 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8773 (pp) REVERT: U 275 HIS cc_start: 0.7732 (m-70) cc_final: 0.7486 (m-70) REVERT: U 307 GLU cc_start: 0.6674 (tt0) cc_final: 0.6462 (tt0) REVERT: X 166 ASN cc_start: 0.8743 (t0) cc_final: 0.8515 (t0) REVERT: X 238 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8936 (pp) REVERT: a 23 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: a 89 MET cc_start: 0.8056 (mtp) cc_final: 0.7742 (mtp) REVERT: a 113 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8402 (ttp80) REVERT: b 112 GLN cc_start: 0.8725 (mt0) cc_final: 0.8512 (mt0) REVERT: b 160 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7014 (mm-30) REVERT: b 176 ASP cc_start: 0.8290 (p0) cc_final: 0.7935 (p0) REVERT: b 194 TYR cc_start: 0.8503 (m-80) cc_final: 0.8139 (m-80) REVERT: c 189 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8272 (ttpp) REVERT: d 22 GLU cc_start: 0.7597 (mp0) cc_final: 0.7285 (mp0) REVERT: d 134 ASP cc_start: 0.6407 (m-30) cc_final: 0.6115 (m-30) REVERT: e 21 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7221 (mmt90) REVERT: f 44 ASN cc_start: 0.9462 (t0) cc_final: 0.9127 (t0) REVERT: f 48 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7648 (mmp-170) REVERT: f 176 ASP cc_start: 0.8121 (p0) cc_final: 0.7810 (p0) REVERT: g 108 SER cc_start: 0.9251 (t) cc_final: 0.8664 (t) REVERT: g 112 GLN cc_start: 0.8774 (mt0) cc_final: 0.8251 (mt0) REVERT: g 176 ASP cc_start: 0.8057 (p0) cc_final: 0.7788 (p0) REVERT: g 194 TYR cc_start: 0.8589 (m-80) cc_final: 0.8282 (m-80) REVERT: i 26 SER cc_start: 0.9103 (p) cc_final: 0.8821 (t) REVERT: i 194 TYR cc_start: 0.8690 (m-80) cc_final: 0.8436 (m-80) REVERT: j 22 GLU cc_start: 0.7621 (mp0) cc_final: 0.7371 (mp0) REVERT: j 74 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8011 (ttp80) REVERT: j 114 LEU cc_start: 0.9461 (mt) cc_final: 0.9248 (mt) REVERT: j 134 ASP cc_start: 0.6579 (m-30) cc_final: 0.6170 (m-30) REVERT: k 113 ARG cc_start: 0.8743 (ttt90) cc_final: 0.8209 (ttt180) REVERT: l 44 ASN cc_start: 0.9405 (t0) cc_final: 0.9086 (t0) REVERT: l 103 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8759 (mtmt) REVERT: l 129 ILE cc_start: 0.8671 (mm) cc_final: 0.8369 (mm) REVERT: l 176 ASP cc_start: 0.8021 (p0) cc_final: 0.7772 (p0) REVERT: m 22 GLU cc_start: 0.7531 (mp0) cc_final: 0.7277 (mp0) REVERT: m 46 THR cc_start: 0.8918 (p) cc_final: 0.8630 (p) REVERT: n 107 TYR cc_start: 0.9197 (m-80) cc_final: 0.8935 (m-10) REVERT: n 112 GLN cc_start: 0.8833 (mt0) cc_final: 0.8397 (mt0) REVERT: n 176 ASP cc_start: 0.8036 (p0) cc_final: 0.7704 (p0) REVERT: o 145 MET cc_start: 0.8240 (tpp) cc_final: 0.8009 (tpp) REVERT: o 194 TYR cc_start: 0.8791 (m-80) cc_final: 0.8525 (m-80) REVERT: q 113 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8610 (ttp80) REVERT: r 176 ASP cc_start: 0.8067 (p0) cc_final: 0.7785 (p0) REVERT: s 74 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7957 (ttp80) REVERT: s 176 ASP cc_start: 0.8246 (p0) cc_final: 0.8006 (p0) REVERT: t 107 TYR cc_start: 0.9148 (m-80) cc_final: 0.8879 (m-10) REVERT: u 26 SER cc_start: 0.9171 (p) cc_final: 0.8942 (t) REVERT: v 128 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8780 (mmtm) REVERT: v 176 ASP cc_start: 0.8094 (p0) cc_final: 0.7847 (p0) REVERT: w 46 THR cc_start: 0.8934 (p) cc_final: 0.8684 (p) REVERT: w 194 TYR cc_start: 0.8698 (m-80) cc_final: 0.8297 (m-80) REVERT: x 26 SER cc_start: 0.9156 (p) cc_final: 0.8882 (t) outliers start: 221 outliers final: 164 residues processed: 1821 average time/residue: 0.7428 time to fit residues: 2210.9333 Evaluate side-chains 1803 residues out of total 8064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1605 time to evaluate : 6.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 161 ARG Chi-restraints excluded: chain S residue 196 CYS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain T residue 223 TYR Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 338 LEU Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 307 GLU Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 296 CYS Chi-restraints excluded: chain Q residue 302 THR Chi-restraints excluded: chain P residue 170 CYS Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 296 CYS Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 247 ASP Chi-restraints excluded: chain N residue 296 CYS Chi-restraints excluded: chain N residue 331 GLN Chi-restraints excluded: chain N residue 338 LEU Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 223 TYR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 296 CYS Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 307 GLU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 336 SER Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 247 ASP Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 336 SER Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 223 TYR Chi-restraints excluded: chain W residue 238 LEU Chi-restraints excluded: chain W residue 296 CYS Chi-restraints excluded: chain W residue 307 GLU Chi-restraints excluded: chain V residue 174 LEU Chi-restraints excluded: chain V residue 223 TYR Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 296 CYS Chi-restraints excluded: chain V residue 302 THR Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain U residue 248 THR Chi-restraints excluded: chain U residue 302 THR Chi-restraints excluded: chain X residue 238 LEU Chi-restraints excluded: chain X residue 334 GLU Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 113 ARG Chi-restraints excluded: chain a residue 116 GLN Chi-restraints excluded: chain a residue 163 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 193 VAL Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 41 GLU Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 155 SER Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 116 GLN Chi-restraints excluded: chain e residue 149 VAL Chi-restraints excluded: chain e residue 163 VAL Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain f residue 163 VAL Chi-restraints excluded: chain g residue 145 MET Chi-restraints excluded: chain g residue 149 VAL Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain h residue 163 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 163 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 58 SER Chi-restraints excluded: chain j residue 61 VAL Chi-restraints excluded: chain j residue 92 THR Chi-restraints excluded: chain j residue 108 SER Chi-restraints excluded: chain j residue 155 SER Chi-restraints excluded: chain j residue 163 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 116 GLN Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 193 VAL Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain m residue 23 GLU Chi-restraints excluded: chain m residue 145 MET Chi-restraints excluded: chain m residue 149 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 163 VAL Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 163 VAL Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 163 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 149 VAL Chi-restraints excluded: chain p residue 155 SER Chi-restraints excluded: chain p residue 186 LEU Chi-restraints excluded: chain q residue 113 ARG Chi-restraints excluded: chain q residue 116 GLN Chi-restraints excluded: chain q residue 149 VAL Chi-restraints excluded: chain q residue 163 VAL Chi-restraints excluded: chain q residue 193 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 159 SER Chi-restraints excluded: chain r residue 163 VAL Chi-restraints excluded: chain s residue 23 GLU Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain s residue 119 VAL Chi-restraints excluded: chain s residue 149 VAL Chi-restraints excluded: chain s residue 163 VAL Chi-restraints excluded: chain s residue 186 LEU Chi-restraints excluded: chain t residue 163 VAL Chi-restraints excluded: chain t residue 186 LEU Chi-restraints excluded: chain u residue 132 SER Chi-restraints excluded: chain u residue 163 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 58 SER Chi-restraints excluded: chain v residue 108 SER Chi-restraints excluded: chain v residue 148 SER Chi-restraints excluded: chain v residue 159 SER Chi-restraints excluded: chain v residue 163 VAL Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 92 THR Chi-restraints excluded: chain w residue 108 SER Chi-restraints excluded: chain w residue 149 VAL Chi-restraints excluded: chain x residue 25 ILE Chi-restraints excluded: chain x residue 155 SER Chi-restraints excluded: chain x residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 1.9990 chunk 709 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 614 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 185 optimal weight: 0.3980 chunk 667 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 685 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 331 GLN Q 166 ASN Q 210 GLN M 318 ASN G 275 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 331 GLN U 210 GLN a 88 GLN b 60 GLN b 196 ASN d 112 GLN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 60 GLN j 88 GLN l 60 GLN n 88 GLN n 112 GLN p 88 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.087557 restraints weight = 105204.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091393 restraints weight = 58317.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.093973 restraints weight = 39709.214| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1248 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 127 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 72024 Z= 0.243 Angle : 0.578 9.572 97224 Z= 0.305 Chirality : 0.045 0.215 11208 Planarity : 0.003 0.056 12456 Dihedral : 4.143 23.766 9600 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.75 % Allowed : 16.84 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8688 helix: 2.38 (0.09), residues: 3456 sheet: 0.18 (0.11), residues: 2184 loop : -1.86 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 183 HIS 0.004 0.001 HIS Q 275 PHE 0.010 0.001 PHE E 285 TYR 0.025 0.001 TYR B 328 ARG 0.008 0.001 ARG C 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29426.58 seconds wall clock time: 502 minutes 45.40 seconds (30165.40 seconds total)