Starting phenix.real_space_refine on Sun Sep 29 04:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/09_2024/5tcp_8398_neut.cif" } resolution = 4.3 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= 0.011 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 45984 2.51 5 N 12912 2.21 5 O 13824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72888 Number of models: 1 Model: "" Number of chains: 2 Chain: "0" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "1" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Restraints were copied for chains: 3, 5, 7, 9, A, C, E, G, I, K, M, O, Q, S, U, W, Y, b, d, f, h, j, l, 2, 4, 6, 8, B, D, F, H, J, L, N, P, R, T, V, X, Z, a, c, e, g, i, k Time building chain proxies: 12.34, per 1000 atoms: 0.17 Number of scatterers: 72888 At special positions: 0 Unit cell: (261.63, 261.63, 78.66, 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 13824 8.00 N 12912 7.00 C 45984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.82 Conformation dependent library (CDL) restraints added in 7.1 seconds 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17280 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 120 sheets defined 45.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain '0' and resid 28 through 42 Processing helix chain '0' and resid 52 through 54 No H-bonds generated for 'chain '0' and resid 52 through 54' Processing helix chain '0' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR 0 66 " --> pdb=" O GLU 0 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 0 67 " --> pdb=" O PRO 0 63 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 89 Processing helix chain '0' and resid 97 through 118 Processing helix chain '0' and resid 136 through 140 Processing helix chain '0' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 0 165 " --> pdb=" O ALA 0 161 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP 0 166 " --> pdb=" O HIS 0 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 0 167 " --> pdb=" O GLN 0 163 " (cutoff:3.500A) Processing helix chain '1' and resid 172 through 177 Processing helix chain '1' and resid 180 through 182 No H-bonds generated for 'chain '1' and resid 180 through 182' Processing helix chain '1' and resid 200 through 214 Processing helix chain '1' and resid 225 through 240 Processing helix chain '1' and resid 268 through 283 Processing helix chain '1' and resid 295 through 310 Processing helix chain '1' and resid 332 through 351 Processing helix chain '2' and resid 28 through 42 Processing helix chain '2' and resid 52 through 54 No H-bonds generated for 'chain '2' and resid 52 through 54' Processing helix chain '2' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 2 66 " --> pdb=" O GLU 2 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 2 67 " --> pdb=" O PRO 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 89 Processing helix chain '2' and resid 97 through 118 Processing helix chain '2' and resid 136 through 140 Processing helix chain '2' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 2 165 " --> pdb=" O ALA 2 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 2 166 " --> pdb=" O HIS 2 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 2 167 " --> pdb=" O GLN 2 163 " (cutoff:3.500A) Processing helix chain '3' and resid 172 through 177 Processing helix chain '3' and resid 180 through 182 No H-bonds generated for 'chain '3' and resid 180 through 182' Processing helix chain '3' and resid 200 through 214 Processing helix chain '3' and resid 225 through 240 Processing helix chain '3' and resid 268 through 283 Processing helix chain '3' and resid 295 through 310 Processing helix chain '3' and resid 332 through 351 Processing helix chain '4' and resid 28 through 42 Processing helix chain '4' and resid 52 through 54 No H-bonds generated for 'chain '4' and resid 52 through 54' Processing helix chain '4' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 4 66 " --> pdb=" O GLU 4 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 4 67 " --> pdb=" O PRO 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 89 Processing helix chain '4' and resid 97 through 118 Processing helix chain '4' and resid 136 through 140 Processing helix chain '4' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER 4 165 " --> pdb=" O ALA 4 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 4 166 " --> pdb=" O HIS 4 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 4 167 " --> pdb=" O GLN 4 163 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 177 Processing helix chain '5' and resid 180 through 182 No H-bonds generated for 'chain '5' and resid 180 through 182' Processing helix chain '5' and resid 200 through 214 Processing helix chain '5' and resid 225 through 240 Processing helix chain '5' and resid 268 through 283 Processing helix chain '5' and resid 295 through 310 Processing helix chain '5' and resid 332 through 351 Processing helix chain '6' and resid 28 through 42 Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR 6 66 " --> pdb=" O GLU 6 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA 6 67 " --> pdb=" O PRO 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 84 through 89 Processing helix chain '6' and resid 97 through 118 Processing helix chain '6' and resid 136 through 140 Processing helix chain '6' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 6 165 " --> pdb=" O ALA 6 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 6 166 " --> pdb=" O HIS 6 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 6 167 " --> pdb=" O GLN 6 163 " (cutoff:3.500A) Processing helix chain '7' and resid 172 through 177 Processing helix chain '7' and resid 180 through 182 No H-bonds generated for 'chain '7' and resid 180 through 182' Processing helix chain '7' and resid 200 through 214 Processing helix chain '7' and resid 225 through 240 Processing helix chain '7' and resid 268 through 283 Processing helix chain '7' and resid 295 through 310 Processing helix chain '7' and resid 332 through 351 Processing helix chain '8' and resid 28 through 42 Processing helix chain '8' and resid 52 through 54 No H-bonds generated for 'chain '8' and resid 52 through 54' Processing helix chain '8' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 8 66 " --> pdb=" O GLU 8 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 8 67 " --> pdb=" O PRO 8 63 " (cutoff:3.500A) Processing helix chain '8' and resid 84 through 89 Processing helix chain '8' and resid 97 through 118 Processing helix chain '8' and resid 136 through 140 Processing helix chain '8' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 8 165 " --> pdb=" O ALA 8 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 8 166 " --> pdb=" O HIS 8 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 8 167 " --> pdb=" O GLN 8 163 " (cutoff:3.500A) Processing helix chain '9' and resid 172 through 177 Processing helix chain '9' and resid 180 through 182 No H-bonds generated for 'chain '9' and resid 180 through 182' Processing helix chain '9' and resid 200 through 214 Processing helix chain '9' and resid 225 through 240 Processing helix chain '9' and resid 268 through 283 Processing helix chain '9' and resid 295 through 310 Processing helix chain '9' and resid 332 through 351 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 97 through 118 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 200 through 214 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 268 through 283 Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 332 through 351 Processing helix chain 'D' and resid 28 through 42 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 97 through 118 Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP D 166 " --> pdb=" O HIS D 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 225 through 240 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 295 through 310 Processing helix chain 'E' and resid 332 through 351 Processing helix chain 'F' and resid 28 through 42 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA F 67 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 97 through 118 Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP F 166 " --> pdb=" O HIS F 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 200 through 214 Processing helix chain 'G' and resid 225 through 240 Processing helix chain 'G' and resid 268 through 283 Processing helix chain 'G' and resid 295 through 310 Processing helix chain 'G' and resid 332 through 351 Processing helix chain 'H' and resid 28 through 42 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA H 67 " --> pdb=" O PRO H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 97 through 118 Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP H 166 " --> pdb=" O HIS H 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 200 through 214 Processing helix chain 'I' and resid 225 through 240 Processing helix chain 'I' and resid 268 through 283 Processing helix chain 'I' and resid 295 through 310 Processing helix chain 'I' and resid 332 through 351 Processing helix chain 'J' and resid 28 through 42 Processing helix chain 'J' and resid 52 through 54 No H-bonds generated for 'chain 'J' and resid 52 through 54' Processing helix chain 'J' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA J 67 " --> pdb=" O PRO J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 97 through 118 Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP J 166 " --> pdb=" O HIS J 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE J 167 " --> pdb=" O GLN J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 Processing helix chain 'K' and resid 180 through 182 No H-bonds generated for 'chain 'K' and resid 180 through 182' Processing helix chain 'K' and resid 200 through 214 Processing helix chain 'K' and resid 225 through 240 Processing helix chain 'K' and resid 268 through 283 Processing helix chain 'K' and resid 295 through 310 Processing helix chain 'K' and resid 332 through 351 Processing helix chain 'L' and resid 28 through 42 Processing helix chain 'L' and resid 52 through 54 No H-bonds generated for 'chain 'L' and resid 52 through 54' Processing helix chain 'L' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA L 67 " --> pdb=" O PRO L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 97 through 118 Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP L 166 " --> pdb=" O HIS L 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE L 167 " --> pdb=" O GLN L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 177 Processing helix chain 'M' and resid 180 through 182 No H-bonds generated for 'chain 'M' and resid 180 through 182' Processing helix chain 'M' and resid 200 through 214 Processing helix chain 'M' and resid 225 through 240 Processing helix chain 'M' and resid 268 through 283 Processing helix chain 'M' and resid 295 through 310 Processing helix chain 'M' and resid 332 through 351 Processing helix chain 'N' and resid 28 through 42 Processing helix chain 'N' and resid 52 through 54 No H-bonds generated for 'chain 'N' and resid 52 through 54' Processing helix chain 'N' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA N 67 " --> pdb=" O PRO N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 89 Processing helix chain 'N' and resid 97 through 118 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER N 165 " --> pdb=" O ALA N 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP N 166 " --> pdb=" O HIS N 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE N 167 " --> pdb=" O GLN N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 177 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 200 through 214 Processing helix chain 'O' and resid 225 through 240 Processing helix chain 'O' and resid 268 through 283 Processing helix chain 'O' and resid 295 through 310 Processing helix chain 'O' and resid 332 through 351 Processing helix chain 'P' and resid 28 through 42 Processing helix chain 'P' and resid 52 through 54 No H-bonds generated for 'chain 'P' and resid 52 through 54' Processing helix chain 'P' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR P 66 " --> pdb=" O GLU P 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 89 Processing helix chain 'P' and resid 97 through 118 Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER P 165 " --> pdb=" O ALA P 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP P 166 " --> pdb=" O HIS P 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE P 167 " --> pdb=" O GLN P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 177 Processing helix chain 'Q' and resid 180 through 182 No H-bonds generated for 'chain 'Q' and resid 180 through 182' Processing helix chain 'Q' and resid 200 through 214 Processing helix chain 'Q' and resid 225 through 240 Processing helix chain 'Q' and resid 268 through 283 Processing helix chain 'Q' and resid 295 through 310 Processing helix chain 'Q' and resid 332 through 351 Processing helix chain 'R' and resid 28 through 42 Processing helix chain 'R' and resid 52 through 54 No H-bonds generated for 'chain 'R' and resid 52 through 54' Processing helix chain 'R' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR R 66 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA R 67 " --> pdb=" O PRO R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 97 through 118 Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 177 Processing helix chain 'S' and resid 180 through 182 No H-bonds generated for 'chain 'S' and resid 180 through 182' Processing helix chain 'S' and resid 200 through 214 Processing helix chain 'S' and resid 225 through 240 Processing helix chain 'S' and resid 268 through 283 Processing helix chain 'S' and resid 295 through 310 Processing helix chain 'S' and resid 332 through 351 Processing helix chain 'T' and resid 28 through 42 Processing helix chain 'T' and resid 52 through 54 No H-bonds generated for 'chain 'T' and resid 52 through 54' Processing helix chain 'T' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR T 66 " --> pdb=" O GLU T 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA T 67 " --> pdb=" O PRO T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 89 Processing helix chain 'T' and resid 97 through 118 Processing helix chain 'T' and resid 136 through 140 Processing helix chain 'T' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER T 165 " --> pdb=" O ALA T 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP T 166 " --> pdb=" O HIS T 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE T 167 " --> pdb=" O GLN T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 177 Processing helix chain 'U' and resid 180 through 182 No H-bonds generated for 'chain 'U' and resid 180 through 182' Processing helix chain 'U' and resid 200 through 214 Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 268 through 283 Processing helix chain 'U' and resid 295 through 310 Processing helix chain 'U' and resid 332 through 351 Processing helix chain 'V' and resid 28 through 42 Processing helix chain 'V' and resid 52 through 54 No H-bonds generated for 'chain 'V' and resid 52 through 54' Processing helix chain 'V' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR V 66 " --> pdb=" O GLU V 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA V 67 " --> pdb=" O PRO V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 89 Processing helix chain 'V' and resid 97 through 118 Processing helix chain 'V' and resid 136 through 140 Processing helix chain 'V' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP V 166 " --> pdb=" O HIS V 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE V 167 " --> pdb=" O GLN V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 177 Processing helix chain 'W' and resid 180 through 182 No H-bonds generated for 'chain 'W' and resid 180 through 182' Processing helix chain 'W' and resid 200 through 214 Processing helix chain 'W' and resid 225 through 240 Processing helix chain 'W' and resid 268 through 283 Processing helix chain 'W' and resid 295 through 310 Processing helix chain 'W' and resid 332 through 351 Processing helix chain 'X' and resid 28 through 42 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR X 66 " --> pdb=" O GLU X 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA X 67 " --> pdb=" O PRO X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 89 Processing helix chain 'X' and resid 97 through 118 Processing helix chain 'X' and resid 136 through 140 Processing helix chain 'X' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER X 165 " --> pdb=" O ALA X 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP X 166 " --> pdb=" O HIS X 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE X 167 " --> pdb=" O GLN X 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 177 Processing helix chain 'Y' and resid 180 through 182 No H-bonds generated for 'chain 'Y' and resid 180 through 182' Processing helix chain 'Y' and resid 200 through 214 Processing helix chain 'Y' and resid 225 through 240 Processing helix chain 'Y' and resid 268 through 283 Processing helix chain 'Y' and resid 295 through 310 Processing helix chain 'Y' and resid 332 through 351 Processing helix chain 'Z' and resid 28 through 42 Processing helix chain 'Z' and resid 52 through 54 No H-bonds generated for 'chain 'Z' and resid 52 through 54' Processing helix chain 'Z' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA Z 67 " --> pdb=" O PRO Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 89 Processing helix chain 'Z' and resid 97 through 118 Processing helix chain 'Z' and resid 136 through 140 Processing helix chain 'Z' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER Z 165 " --> pdb=" O ALA Z 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP Z 166 " --> pdb=" O HIS Z 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 167 " --> pdb=" O GLN Z 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 42 Processing helix chain 'a' and resid 52 through 54 No H-bonds generated for 'chain 'a' and resid 52 through 54' Processing helix chain 'a' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR a 66 " --> pdb=" O GLU a 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA a 67 " --> pdb=" O PRO a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 Processing helix chain 'a' and resid 97 through 118 Processing helix chain 'a' and resid 136 through 140 Processing helix chain 'a' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER a 165 " --> pdb=" O ALA a 161 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP a 166 " --> pdb=" O HIS a 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE a 167 " --> pdb=" O GLN a 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 180 through 182 No H-bonds generated for 'chain 'b' and resid 180 through 182' Processing helix chain 'b' and resid 200 through 214 Processing helix chain 'b' and resid 225 through 240 Processing helix chain 'b' and resid 268 through 283 Processing helix chain 'b' and resid 295 through 310 Processing helix chain 'b' and resid 332 through 351 Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'c' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR c 66 " --> pdb=" O GLU c 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 89 Processing helix chain 'c' and resid 97 through 118 Processing helix chain 'c' and resid 136 through 140 Processing helix chain 'c' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER c 165 " --> pdb=" O ALA c 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE c 167 " --> pdb=" O GLN c 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 177 Processing helix chain 'd' and resid 180 through 182 No H-bonds generated for 'chain 'd' and resid 180 through 182' Processing helix chain 'd' and resid 200 through 214 Processing helix chain 'd' and resid 225 through 240 Processing helix chain 'd' and resid 268 through 283 Processing helix chain 'd' and resid 295 through 310 Processing helix chain 'd' and resid 332 through 351 Processing helix chain 'e' and resid 28 through 42 Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR e 66 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA e 67 " --> pdb=" O PRO e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 97 through 118 Processing helix chain 'e' and resid 136 through 140 Processing helix chain 'e' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER e 165 " --> pdb=" O ALA e 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP e 166 " --> pdb=" O HIS e 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE e 167 " --> pdb=" O GLN e 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 177 Processing helix chain 'f' and resid 180 through 182 No H-bonds generated for 'chain 'f' and resid 180 through 182' Processing helix chain 'f' and resid 200 through 214 Processing helix chain 'f' and resid 225 through 240 Processing helix chain 'f' and resid 268 through 283 Processing helix chain 'f' and resid 295 through 310 Processing helix chain 'f' and resid 332 through 351 Processing helix chain 'g' and resid 28 through 42 Processing helix chain 'g' and resid 52 through 54 No H-bonds generated for 'chain 'g' and resid 52 through 54' Processing helix chain 'g' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA g 67 " --> pdb=" O PRO g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 89 Processing helix chain 'g' and resid 97 through 118 Processing helix chain 'g' and resid 136 through 140 Processing helix chain 'g' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER g 165 " --> pdb=" O ALA g 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP g 166 " --> pdb=" O HIS g 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE g 167 " --> pdb=" O GLN g 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 177 Processing helix chain 'h' and resid 180 through 182 No H-bonds generated for 'chain 'h' and resid 180 through 182' Processing helix chain 'h' and resid 200 through 214 Processing helix chain 'h' and resid 225 through 240 Processing helix chain 'h' and resid 268 through 283 Processing helix chain 'h' and resid 295 through 310 Processing helix chain 'h' and resid 332 through 351 Processing helix chain 'i' and resid 28 through 42 Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR i 66 " --> pdb=" O GLU i 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA i 67 " --> pdb=" O PRO i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 89 Processing helix chain 'i' and resid 97 through 118 Processing helix chain 'i' and resid 136 through 140 Processing helix chain 'i' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER i 165 " --> pdb=" O ALA i 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP i 166 " --> pdb=" O HIS i 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE i 167 " --> pdb=" O GLN i 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 172 through 177 Processing helix chain 'j' and resid 180 through 182 No H-bonds generated for 'chain 'j' and resid 180 through 182' Processing helix chain 'j' and resid 200 through 214 Processing helix chain 'j' and resid 225 through 240 Processing helix chain 'j' and resid 268 through 283 Processing helix chain 'j' and resid 295 through 310 Processing helix chain 'j' and resid 332 through 351 Processing helix chain 'k' and resid 28 through 42 Processing helix chain 'k' and resid 52 through 54 No H-bonds generated for 'chain 'k' and resid 52 through 54' Processing helix chain 'k' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR k 66 " --> pdb=" O GLU k 62 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA k 67 " --> pdb=" O PRO k 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 89 Processing helix chain 'k' and resid 97 through 118 Processing helix chain 'k' and resid 136 through 140 Processing helix chain 'k' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER k 165 " --> pdb=" O ALA k 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP k 166 " --> pdb=" O HIS k 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE k 167 " --> pdb=" O GLN k 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 172 through 177 Processing helix chain 'l' and resid 180 through 182 No H-bonds generated for 'chain 'l' and resid 180 through 182' Processing helix chain 'l' and resid 200 through 214 Processing helix chain 'l' and resid 225 through 240 Processing helix chain 'l' and resid 268 through 283 Processing helix chain 'l' and resid 295 through 310 Processing helix chain 'l' and resid 332 through 351 Processing sheet with id=AA1, first strand: chain '0' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 0 58 " --> pdb=" O LEU 0 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 0 25 " --> pdb=" O TYR 0 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 0 56 " --> pdb=" O LYS 0 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL 0 153 " --> pdb=" O LEU 0 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 0 126 " --> pdb=" O LEU 0 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 0 151 " --> pdb=" O ALA 0 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 0 128 " --> pdb=" O SER 0 149 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER 0 149 " --> pdb=" O VAL 0 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 0 148 " --> pdb=" O SER 0 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 0 186 " --> pdb=" O LEU 0 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 0 150 " --> pdb=" O VAL 0 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER 0 188 " --> pdb=" O ALA 0 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 0 152 " --> pdb=" O SER 0 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 1 194 " --> pdb=" O ARG 1 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 1 223 " --> pdb=" O LEU 1 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 1 196 " --> pdb=" O ILE 1 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 1 245 " --> pdb=" O SER 1 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 1 261 " --> pdb=" O TYR 1 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 1 247 " --> pdb=" O TRP 1 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 1 258 " --> pdb=" O THR 1 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 1 294 " --> pdb=" O PHE 1 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 1 260 " --> pdb=" O MET 1 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL 1 323 " --> pdb=" O GLN 1 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 1 358 " --> pdb=" O VAL 1 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 1 325 " --> pdb=" O ALA 1 358 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU 1 360 " --> pdb=" O PHE 1 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 1 327 " --> pdb=" O GLU 1 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 2 58 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 2 25 " --> pdb=" O TYR 2 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 2 56 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 2 153 " --> pdb=" O LEU 2 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA 2 126 " --> pdb=" O LEU 2 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 2 151 " --> pdb=" O ALA 2 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL 2 128 " --> pdb=" O SER 2 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 2 149 " --> pdb=" O VAL 2 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 2 148 " --> pdb=" O SER 2 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL 2 186 " --> pdb=" O LEU 2 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 2 150 " --> pdb=" O VAL 2 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER 2 188 " --> pdb=" O ALA 2 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 2 152 " --> pdb=" O SER 2 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 3 194 " --> pdb=" O ARG 3 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 3 223 " --> pdb=" O LEU 3 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 3 245 " --> pdb=" O SER 3 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER 3 261 " --> pdb=" O TYR 3 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 3 247 " --> pdb=" O TRP 3 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 3 258 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 3 294 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 3 260 " --> pdb=" O MET 3 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL 3 323 " --> pdb=" O GLN 3 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 3 358 " --> pdb=" O VAL 3 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 3 325 " --> pdb=" O ALA 3 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU 3 360 " --> pdb=" O PHE 3 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 3 327 " --> pdb=" O GLU 3 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 4 58 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS 4 25 " --> pdb=" O TYR 4 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR 4 56 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 4 153 " --> pdb=" O LEU 4 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 4 126 " --> pdb=" O LEU 4 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 4 151 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 4 128 " --> pdb=" O SER 4 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 4 149 " --> pdb=" O VAL 4 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 4 148 " --> pdb=" O SER 4 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 4 186 " --> pdb=" O LEU 4 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 4 150 " --> pdb=" O VAL 4 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 4 188 " --> pdb=" O ALA 4 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 4 152 " --> pdb=" O SER 4 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 5 194 " --> pdb=" O ARG 5 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE 5 223 " --> pdb=" O LEU 5 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 5 196 " --> pdb=" O ILE 5 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 5 245 " --> pdb=" O SER 5 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 5 261 " --> pdb=" O TYR 5 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 5 247 " --> pdb=" O TRP 5 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE 5 258 " --> pdb=" O THR 5 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 5 294 " --> pdb=" O PHE 5 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 5 260 " --> pdb=" O MET 5 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL 5 323 " --> pdb=" O GLN 5 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA 5 358 " --> pdb=" O VAL 5 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 5 325 " --> pdb=" O ALA 5 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU 5 360 " --> pdb=" O PHE 5 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 5 327 " --> pdb=" O GLU 5 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 6 58 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 6 25 " --> pdb=" O TYR 6 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 6 56 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 6 153 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 6 126 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 6 151 " --> pdb=" O ALA 6 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL 6 128 " --> pdb=" O SER 6 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 6 149 " --> pdb=" O VAL 6 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU 6 148 " --> pdb=" O SER 6 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 6 186 " --> pdb=" O LEU 6 148 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA 6 150 " --> pdb=" O VAL 6 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 6 188 " --> pdb=" O ALA 6 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 6 152 " --> pdb=" O SER 6 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 7 194 " --> pdb=" O ARG 7 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 7 223 " --> pdb=" O LEU 7 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 7 196 " --> pdb=" O ILE 7 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '7' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 7 245 " --> pdb=" O SER 7 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 7 261 " --> pdb=" O TYR 7 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 7 247 " --> pdb=" O TRP 7 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE 7 258 " --> pdb=" O THR 7 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET 7 294 " --> pdb=" O PHE 7 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 7 260 " --> pdb=" O MET 7 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL 7 323 " --> pdb=" O GLN 7 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA 7 358 " --> pdb=" O VAL 7 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 7 325 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU 7 360 " --> pdb=" O PHE 7 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 7 327 " --> pdb=" O GLU 7 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '8' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 8 58 " --> pdb=" O LEU 8 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 8 25 " --> pdb=" O TYR 8 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 8 56 " --> pdb=" O LYS 8 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '8' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 8 153 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 8 126 " --> pdb=" O LEU 8 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 8 151 " --> pdb=" O ALA 8 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 8 128 " --> pdb=" O SER 8 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 8 149 " --> pdb=" O VAL 8 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 8 148 " --> pdb=" O SER 8 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 8 186 " --> pdb=" O LEU 8 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA 8 150 " --> pdb=" O VAL 8 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 8 188 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA 8 152 " --> pdb=" O SER 8 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '9' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU 9 194 " --> pdb=" O ARG 9 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 9 223 " --> pdb=" O LEU 9 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL 9 196 " --> pdb=" O ILE 9 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '9' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR 9 245 " --> pdb=" O SER 9 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER 9 261 " --> pdb=" O TYR 9 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 9 247 " --> pdb=" O TRP 9 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 9 258 " --> pdb=" O THR 9 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 9 294 " --> pdb=" O PHE 9 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 9 260 " --> pdb=" O MET 9 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '9' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL 9 323 " --> pdb=" O GLN 9 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 9 358 " --> pdb=" O VAL 9 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 9 325 " --> pdb=" O ALA 9 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU 9 360 " --> pdb=" O PHE 9 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 9 327 " --> pdb=" O GLU 9 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU A 194 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE A 223 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 196 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR A 245 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER A 261 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 247 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 258 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 294 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 260 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL A 323 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 358 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 325 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU A 360 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 327 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE B 58 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 25 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 56 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL B 153 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 126 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 151 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL B 128 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER B 149 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 148 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL B 186 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA B 150 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER B 188 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 152 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU C 194 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE C 223 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 196 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR C 245 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 261 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG C 247 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE C 258 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET C 294 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU C 260 " --> pdb=" O MET C 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL C 323 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA C 358 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE C 325 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU C 360 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 327 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE D 58 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS D 25 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR D 56 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL D 153 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 126 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 151 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 128 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER D 149 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 148 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL D 186 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA D 150 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER D 188 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA D 152 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU E 194 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE E 223 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 196 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR E 245 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER E 261 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG E 247 " --> pdb=" O TRP E 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE E 258 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET E 294 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 260 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL E 323 " --> pdb=" O GLN E 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA E 358 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE E 325 " --> pdb=" O ALA E 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU E 360 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE E 327 " --> pdb=" O GLU E 360 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE F 58 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS F 25 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR F 56 " --> pdb=" O LYS F 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL F 153 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA F 126 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 151 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 128 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER F 149 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU F 148 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL F 186 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA F 150 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER F 188 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA F 152 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU G 194 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE G 223 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL G 196 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR G 245 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG G 247 " --> pdb=" O TRP G 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE G 258 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET G 294 " --> pdb=" O PHE G 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU G 260 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL G 323 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA G 358 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE G 325 " --> pdb=" O ALA G 358 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU G 360 " --> pdb=" O PHE G 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE G 327 " --> pdb=" O GLU G 360 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE H 58 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS H 25 " --> pdb=" O TYR H 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR H 56 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL H 153 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA H 126 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 151 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL H 128 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER H 149 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU H 148 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL H 186 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA H 150 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER H 188 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA H 152 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU I 194 " --> pdb=" O ARG I 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE I 223 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL I 196 " --> pdb=" O ILE I 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR I 245 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER I 261 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG I 247 " --> pdb=" O TRP I 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE I 258 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET I 294 " --> pdb=" O PHE I 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU I 260 " --> pdb=" O MET I 294 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL I 323 " --> pdb=" O GLN I 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA I 358 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE I 325 " --> pdb=" O ALA I 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU I 360 " --> pdb=" O PHE I 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE I 327 " --> pdb=" O GLU I 360 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE J 58 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS J 25 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR J 56 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL J 153 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA J 126 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU J 151 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL J 128 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER J 149 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU J 148 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL J 186 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA J 150 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER J 188 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA J 152 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU K 194 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE K 223 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL K 196 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR K 245 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER K 261 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG K 247 " --> pdb=" O TRP K 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE K 258 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET K 294 " --> pdb=" O PHE K 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 260 " --> pdb=" O MET K 294 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL K 323 " --> pdb=" O GLN K 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA K 358 " --> pdb=" O VAL K 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE K 325 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU K 360 " --> pdb=" O PHE K 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE K 327 " --> pdb=" O GLU K 360 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE L 58 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS L 25 " --> pdb=" O TYR L 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR L 56 " --> pdb=" O LYS L 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL L 153 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA L 126 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU L 151 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL L 128 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER L 149 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 148 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL L 186 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA L 150 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER L 188 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA L 152 " --> pdb=" O SER L 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU M 194 " --> pdb=" O ARG M 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE M 223 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL M 196 " --> pdb=" O ILE M 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR M 245 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER M 261 " --> pdb=" O TYR M 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG M 247 " --> pdb=" O TRP M 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE M 258 " --> pdb=" O THR M 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET M 294 " --> pdb=" O PHE M 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU M 260 " --> pdb=" O MET M 294 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL M 323 " --> pdb=" O GLN M 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA M 358 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE M 325 " --> pdb=" O ALA M 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU M 360 " --> pdb=" O PHE M 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE M 327 " --> pdb=" O GLU M 360 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE N 58 " --> pdb=" O LEU N 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS N 25 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR N 56 " --> pdb=" O LYS N 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL N 153 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA N 126 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU N 151 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL N 128 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER N 149 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU N 148 " --> pdb=" O SER N 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL N 186 " --> pdb=" O LEU N 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA N 150 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER N 188 " --> pdb=" O ALA N 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA N 152 " --> pdb=" O SER N 188 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU O 194 " --> pdb=" O ARG O 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE O 223 " --> pdb=" O LEU O 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 196 " --> pdb=" O ILE O 223 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR O 245 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER O 261 " --> pdb=" O TYR O 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG O 247 " --> pdb=" O TRP O 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE O 258 " --> pdb=" O THR O 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET O 294 " --> pdb=" O PHE O 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU O 260 " --> pdb=" O MET O 294 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL O 323 " --> pdb=" O GLN O 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA O 358 " --> pdb=" O VAL O 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE O 325 " --> pdb=" O ALA O 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU O 360 " --> pdb=" O PHE O 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE O 327 " --> pdb=" O GLU O 360 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE P 58 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS P 25 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR P 56 " --> pdb=" O LYS P 25 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL P 153 " --> pdb=" O LEU P 124 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA P 126 " --> pdb=" O LEU P 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU P 151 " --> pdb=" O ALA P 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL P 128 " --> pdb=" O SER P 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER P 149 " --> pdb=" O VAL P 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU P 148 " --> pdb=" O SER P 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL P 186 " --> pdb=" O LEU P 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA P 150 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER P 188 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA P 152 " --> pdb=" O SER P 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU Q 194 " --> pdb=" O ARG Q 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE Q 223 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL Q 196 " --> pdb=" O ILE Q 223 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR Q 245 " --> pdb=" O SER Q 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER Q 261 " --> pdb=" O TYR Q 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG Q 247 " --> pdb=" O TRP Q 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE Q 258 " --> pdb=" O THR Q 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET Q 294 " --> pdb=" O PHE Q 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU Q 260 " --> pdb=" O MET Q 294 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL Q 323 " --> pdb=" O GLN Q 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA Q 358 " --> pdb=" O VAL Q 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE Q 325 " --> pdb=" O ALA Q 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU Q 360 " --> pdb=" O PHE Q 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE Q 327 " --> pdb=" O GLU Q 360 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE R 58 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS R 25 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR R 56 " --> pdb=" O LYS R 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL R 153 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA R 126 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU R 151 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL R 128 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER R 149 " --> pdb=" O VAL R 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU R 148 " --> pdb=" O SER R 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL R 186 " --> pdb=" O LEU R 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA R 150 " --> pdb=" O VAL R 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER R 188 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA R 152 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU S 194 " --> pdb=" O ARG S 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE S 223 " --> pdb=" O LEU S 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL S 196 " --> pdb=" O ILE S 223 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'S' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR S 245 " --> pdb=" O SER S 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER S 261 " --> pdb=" O TYR S 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG S 247 " --> pdb=" O TRP S 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE S 258 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET S 294 " --> pdb=" O PHE S 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU S 260 " --> pdb=" O MET S 294 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL S 323 " --> pdb=" O GLN S 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA S 358 " --> pdb=" O VAL S 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE S 325 " --> pdb=" O ALA S 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU S 360 " --> pdb=" O PHE S 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE S 327 " --> pdb=" O GLU S 360 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE T 58 " --> pdb=" O LEU T 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS T 25 " --> pdb=" O TYR T 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR T 56 " --> pdb=" O LYS T 25 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL T 153 " --> pdb=" O LEU T 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA T 126 " --> pdb=" O LEU T 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU T 151 " --> pdb=" O ALA T 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL T 128 " --> pdb=" O SER T 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER T 149 " --> pdb=" O VAL T 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU T 148 " --> pdb=" O SER T 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL T 186 " --> pdb=" O LEU T 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA T 150 " --> pdb=" O VAL T 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER T 188 " --> pdb=" O ALA T 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA T 152 " --> pdb=" O SER T 188 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU U 194 " --> pdb=" O ARG U 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE U 223 " --> pdb=" O LEU U 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL U 196 " --> pdb=" O ILE U 223 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR U 245 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER U 261 " --> pdb=" O TYR U 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG U 247 " --> pdb=" O TRP U 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE U 258 " --> pdb=" O THR U 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET U 294 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU U 260 " --> pdb=" O MET U 294 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL U 323 " --> pdb=" O GLN U 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA U 358 " --> pdb=" O VAL U 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE U 325 " --> pdb=" O ALA U 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU U 360 " --> pdb=" O PHE U 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE U 327 " --> pdb=" O GLU U 360 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE V 58 " --> pdb=" O LEU V 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS V 25 " --> pdb=" O TYR V 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR V 56 " --> pdb=" O LYS V 25 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'V' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL V 153 " --> pdb=" O LEU V 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA V 126 " --> pdb=" O LEU V 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU V 151 " --> pdb=" O ALA V 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL V 128 " --> pdb=" O SER V 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER V 149 " --> pdb=" O VAL V 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU V 148 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL V 186 " --> pdb=" O LEU V 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA V 150 " --> pdb=" O VAL V 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER V 188 " --> pdb=" O ALA V 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA V 152 " --> pdb=" O SER V 188 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU W 194 " --> pdb=" O ARG W 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE W 223 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL W 196 " --> pdb=" O ILE W 223 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR W 245 " --> pdb=" O SER W 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER W 261 " --> pdb=" O TYR W 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG W 247 " --> pdb=" O TRP W 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE W 258 " --> pdb=" O THR W 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET W 294 " --> pdb=" O PHE W 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU W 260 " --> pdb=" O MET W 294 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL W 323 " --> pdb=" O GLN W 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA W 358 " --> pdb=" O VAL W 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE W 325 " --> pdb=" O ALA W 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU W 360 " --> pdb=" O PHE W 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE W 327 " --> pdb=" O GLU W 360 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'X' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE X 58 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS X 25 " --> pdb=" O TYR X 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR X 56 " --> pdb=" O LYS X 25 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'X' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL X 153 " --> pdb=" O LEU X 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA X 126 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU X 151 " --> pdb=" O ALA X 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL X 128 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER X 149 " --> pdb=" O VAL X 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU X 148 " --> pdb=" O SER X 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL X 186 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA X 150 " --> pdb=" O VAL X 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER X 188 " --> pdb=" O ALA X 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA X 152 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Y' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU Y 194 " --> pdb=" O ARG Y 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE Y 223 " --> pdb=" O LEU Y 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL Y 196 " --> pdb=" O ILE Y 223 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR Y 245 " --> pdb=" O SER Y 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER Y 261 " --> pdb=" O TYR Y 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG Y 247 " --> pdb=" O TRP Y 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE Y 258 " --> pdb=" O THR Y 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET Y 294 " --> pdb=" O PHE Y 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU Y 260 " --> pdb=" O MET Y 294 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL Y 323 " --> pdb=" O GLN Y 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA Y 358 " --> pdb=" O VAL Y 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE Y 325 " --> pdb=" O ALA Y 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU Y 360 " --> pdb=" O PHE Y 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE Y 327 " --> pdb=" O GLU Y 360 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Z' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE Z 58 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS Z 25 " --> pdb=" O TYR Z 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR Z 56 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL Z 153 " --> pdb=" O LEU Z 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA Z 126 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU Z 151 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL Z 128 " --> pdb=" O SER Z 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER Z 149 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU Z 148 " --> pdb=" O SER Z 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL Z 186 " --> pdb=" O LEU Z 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA Z 150 " --> pdb=" O VAL Z 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER Z 188 " --> pdb=" O ALA Z 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA Z 152 " --> pdb=" O SER Z 188 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'a' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE a 58 " --> pdb=" O LEU a 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS a 25 " --> pdb=" O TYR a 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR a 56 " --> pdb=" O LYS a 25 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'a' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL a 153 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA a 126 " --> pdb=" O LEU a 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU a 151 " --> pdb=" O ALA a 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL a 128 " --> pdb=" O SER a 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER a 149 " --> pdb=" O VAL a 128 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU a 148 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL a 186 " --> pdb=" O LEU a 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA a 150 " --> pdb=" O VAL a 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER a 188 " --> pdb=" O ALA a 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA a 152 " --> pdb=" O SER a 188 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'b' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU b 194 " --> pdb=" O ARG b 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE b 223 " --> pdb=" O LEU b 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL b 196 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR b 245 " --> pdb=" O SER b 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER b 261 " --> pdb=" O TYR b 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG b 247 " --> pdb=" O TRP b 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE b 258 " --> pdb=" O THR b 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET b 294 " --> pdb=" O PHE b 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU b 260 " --> pdb=" O MET b 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL b 323 " --> pdb=" O GLN b 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA b 358 " --> pdb=" O VAL b 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE b 325 " --> pdb=" O ALA b 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU b 360 " --> pdb=" O PHE b 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE b 327 " --> pdb=" O GLU b 360 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'c' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE c 58 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS c 25 " --> pdb=" O TYR c 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR c 56 " --> pdb=" O LYS c 25 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'c' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL c 153 " --> pdb=" O LEU c 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA c 126 " --> pdb=" O LEU c 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU c 151 " --> pdb=" O ALA c 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL c 128 " --> pdb=" O SER c 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER c 149 " --> pdb=" O VAL c 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU c 148 " --> pdb=" O SER c 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL c 186 " --> pdb=" O LEU c 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA c 150 " --> pdb=" O VAL c 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER c 188 " --> pdb=" O ALA c 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA c 152 " --> pdb=" O SER c 188 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'd' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU d 194 " --> pdb=" O ARG d 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE d 223 " --> pdb=" O LEU d 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL d 196 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'd' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR d 245 " --> pdb=" O SER d 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER d 261 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG d 247 " --> pdb=" O TRP d 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE d 258 " --> pdb=" O THR d 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET d 294 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU d 260 " --> pdb=" O MET d 294 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'd' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL d 323 " --> pdb=" O GLN d 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA d 358 " --> pdb=" O VAL d 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE d 325 " --> pdb=" O ALA d 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU d 360 " --> pdb=" O PHE d 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE d 327 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'e' and resid 21 through 27 removed outlier: 6.550A pdb=" N ILE e 58 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS e 25 " --> pdb=" O TYR e 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR e 56 " --> pdb=" O LYS e 25 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'e' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL e 153 " --> pdb=" O LEU e 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA e 126 " --> pdb=" O LEU e 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU e 151 " --> pdb=" O ALA e 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL e 128 " --> pdb=" O SER e 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER e 149 " --> pdb=" O VAL e 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU e 148 " --> pdb=" O SER e 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL e 186 " --> pdb=" O LEU e 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA e 150 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER e 188 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA e 152 " --> pdb=" O SER e 188 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'f' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU f 194 " --> pdb=" O ARG f 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE f 223 " --> pdb=" O LEU f 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL f 196 " --> pdb=" O ILE f 223 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'f' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR f 245 " --> pdb=" O SER f 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER f 261 " --> pdb=" O TYR f 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG f 247 " --> pdb=" O TRP f 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE f 258 " --> pdb=" O THR f 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET f 294 " --> pdb=" O PHE f 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU f 260 " --> pdb=" O MET f 294 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'f' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL f 323 " --> pdb=" O GLN f 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA f 358 " --> pdb=" O VAL f 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE f 325 " --> pdb=" O ALA f 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU f 360 " --> pdb=" O PHE f 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE f 327 " --> pdb=" O GLU f 360 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'g' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE g 58 " --> pdb=" O LEU g 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS g 25 " --> pdb=" O TYR g 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR g 56 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'g' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL g 153 " --> pdb=" O LEU g 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA g 126 " --> pdb=" O LEU g 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU g 151 " --> pdb=" O ALA g 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL g 128 " --> pdb=" O SER g 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER g 149 " --> pdb=" O VAL g 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU g 148 " --> pdb=" O SER g 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL g 186 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA g 150 " --> pdb=" O VAL g 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER g 188 " --> pdb=" O ALA g 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA g 152 " --> pdb=" O SER g 188 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'h' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU h 194 " --> pdb=" O ARG h 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE h 223 " --> pdb=" O LEU h 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL h 196 " --> pdb=" O ILE h 223 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'h' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR h 245 " --> pdb=" O SER h 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER h 261 " --> pdb=" O TYR h 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG h 247 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE h 258 " --> pdb=" O THR h 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET h 294 " --> pdb=" O PHE h 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU h 260 " --> pdb=" O MET h 294 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'h' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL h 323 " --> pdb=" O GLN h 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA h 358 " --> pdb=" O VAL h 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE h 325 " --> pdb=" O ALA h 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU h 360 " --> pdb=" O PHE h 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE h 327 " --> pdb=" O GLU h 360 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'i' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE i 58 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS i 25 " --> pdb=" O TYR i 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR i 56 " --> pdb=" O LYS i 25 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'i' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL i 153 " --> pdb=" O LEU i 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA i 126 " --> pdb=" O LEU i 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU i 151 " --> pdb=" O ALA i 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL i 128 " --> pdb=" O SER i 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER i 149 " --> pdb=" O VAL i 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU i 148 " --> pdb=" O SER i 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL i 186 " --> pdb=" O LEU i 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA i 150 " --> pdb=" O VAL i 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER i 188 " --> pdb=" O ALA i 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA i 152 " --> pdb=" O SER i 188 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'j' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU j 194 " --> pdb=" O ARG j 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE j 223 " --> pdb=" O LEU j 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL j 196 " --> pdb=" O ILE j 223 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'j' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR j 245 " --> pdb=" O SER j 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER j 261 " --> pdb=" O TYR j 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG j 247 " --> pdb=" O TRP j 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE j 258 " --> pdb=" O THR j 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET j 294 " --> pdb=" O PHE j 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU j 260 " --> pdb=" O MET j 294 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'j' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL j 323 " --> pdb=" O GLN j 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA j 358 " --> pdb=" O VAL j 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE j 325 " --> pdb=" O ALA j 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU j 360 " --> pdb=" O PHE j 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE j 327 " --> pdb=" O GLU j 360 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'k' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE k 58 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS k 25 " --> pdb=" O TYR k 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR k 56 " --> pdb=" O LYS k 25 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'k' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL k 153 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA k 126 " --> pdb=" O LEU k 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU k 151 " --> pdb=" O ALA k 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL k 128 " --> pdb=" O SER k 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER k 149 " --> pdb=" O VAL k 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU k 148 " --> pdb=" O SER k 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL k 186 " --> pdb=" O LEU k 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA k 150 " --> pdb=" O VAL k 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER k 188 " --> pdb=" O ALA k 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA k 152 " --> pdb=" O SER k 188 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'l' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU l 194 " --> pdb=" O ARG l 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE l 223 " --> pdb=" O LEU l 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL l 196 " --> pdb=" O ILE l 223 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'l' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR l 245 " --> pdb=" O SER l 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER l 261 " --> pdb=" O TYR l 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG l 247 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE l 258 " --> pdb=" O THR l 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET l 294 " --> pdb=" O PHE l 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU l 260 " --> pdb=" O MET l 294 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'l' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL l 323 " --> pdb=" O GLN l 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA l 358 " --> pdb=" O VAL l 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE l 325 " --> pdb=" O ALA l 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU l 360 " --> pdb=" O PHE l 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE l 327 " --> pdb=" O GLU l 360 " (cutoff:3.500A) 3288 hydrogen bonds defined for protein. 9144 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: 27.28 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16349 1.32 - 1.44: 16071 1.44 - 1.56: 41572 1.56 - 1.68: 0 1.68 - 1.80: 336 Bond restraints: 74328 Sorted by residual: bond pdb=" CA ASP F 166 " pdb=" C ASP F 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.67e+00 bond pdb=" CA ASP R 166 " pdb=" C ASP R 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.66e+00 bond pdb=" CA ASP 6 166 " pdb=" C ASP 6 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.65e+00 bond pdb=" CA ASP N 166 " pdb=" C ASP N 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" CA ASP c 166 " pdb=" C ASP c 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.59e+00 ... (remaining 74323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 91510 2.19 - 4.38: 7811 4.38 - 6.56: 927 6.56 - 8.75: 311 8.75 - 10.94: 73 Bond angle restraints: 100632 Sorted by residual: angle pdb=" C ARG F 141 " pdb=" N PRO F 142 " pdb=" CA PRO F 142 " ideal model delta sigma weight residual 119.66 127.08 -7.42 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG 0 141 " pdb=" N PRO 0 142 " pdb=" CA PRO 0 142 " ideal model delta sigma weight residual 119.66 127.08 -7.42 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG 2 141 " pdb=" N PRO 2 142 " pdb=" CA PRO 2 142 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG N 141 " pdb=" N PRO N 142 " pdb=" CA PRO N 142 " ideal model delta sigma weight residual 119.66 127.06 -7.40 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG B 141 " pdb=" N PRO B 142 " pdb=" CA PRO B 142 " ideal model delta sigma weight residual 119.66 127.05 -7.39 7.20e-01 1.93e+00 1.05e+02 ... (remaining 100627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 43080 13.43 - 26.85: 1726 26.85 - 40.28: 314 40.28 - 53.71: 288 53.71 - 67.13: 168 Dihedral angle restraints: 45576 sinusoidal: 18840 harmonic: 26736 Sorted by residual: dihedral pdb=" CG ARG C 280 " pdb=" CD ARG C 280 " pdb=" NE ARG C 280 " pdb=" CZ ARG C 280 " ideal model delta sinusoidal sigma weight residual 180.00 -144.86 -35.14 2 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CG ARG 7 280 " pdb=" CD ARG 7 280 " pdb=" NE ARG 7 280 " pdb=" CZ ARG 7 280 " ideal model delta sinusoidal sigma weight residual -180.00 -144.87 -35.13 2 1.50e+01 4.44e-03 7.06e+00 dihedral pdb=" CG ARG 5 280 " pdb=" CD ARG 5 280 " pdb=" NE ARG 5 280 " pdb=" CZ ARG 5 280 " ideal model delta sinusoidal sigma weight residual 180.00 -144.88 -35.12 2 1.50e+01 4.44e-03 7.06e+00 ... (remaining 45573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5432 0.045 - 0.090: 3697 0.090 - 0.135: 1407 0.135 - 0.180: 346 0.180 - 0.225: 62 Chirality restraints: 10944 Sorted by residual: chirality pdb=" CA ASN i 173 " pdb=" N ASN i 173 " pdb=" C ASN i 173 " pdb=" CB ASN i 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASN 4 173 " pdb=" N ASN 4 173 " pdb=" C ASN 4 173 " pdb=" CB ASN 4 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 10941 not shown) Planarity restraints: 13248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO C 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO Y 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO Y 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO Y 188 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU f 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO f 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO f 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO f 188 " -0.067 5.00e-02 4.00e+02 ... (remaining 13245 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 36172 2.96 - 3.45: 70443 3.45 - 3.93: 120116 3.93 - 4.42: 136135 4.42 - 4.90: 213399 Nonbonded interactions: 576265 Sorted by model distance: nonbonded pdb=" C ASP 0 28 " pdb=" OD1 ASP 0 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP H 28 " pdb=" OD1 ASP H 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP N 28 " pdb=" OD1 ASP N 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP g 28 " pdb=" OD1 ASP g 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP 6 28 " pdb=" OD1 ASP 6 28 " model vdw 2.479 3.270 ... (remaining 576260 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.070 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: 0.050 Extract box with map and model: 2.250 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 105.180 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.520 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.013 0.055 74328 Z= 0.822 Angle : 1.383 10.941 100632 Z= 0.967 Chirality : 0.066 0.225 10944 Planarity : 0.010 0.131 13248 Dihedral : 9.896 67.134 28296 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 1.07 % Allowed : 3.48 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.87 (0.08), residues: 8976 helix: -0.38 (0.07), residues: 3720 sheet: -0.52 (0.12), residues: 2136 loop : -0.56 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP d 350 HIS 0.004 0.001 HIS l 249 PHE 0.020 0.003 PHE B 175 TYR 0.038 0.005 TYR 1 346 ARG 0.004 0.001 ARG l 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1526 time to evaluate : 6.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 24 LEU cc_start: 0.9137 (mt) cc_final: 0.8812 (mp) REVERT: 0 154 TYR cc_start: 0.8533 (m-80) cc_final: 0.7942 (m-80) REVERT: 1 193 MET cc_start: 0.7917 (ttm) cc_final: 0.7575 (ttm) REVERT: 1 294 MET cc_start: 0.8495 (mmm) cc_final: 0.7891 (mmp) REVERT: 3 294 MET cc_start: 0.8522 (mmm) cc_final: 0.8052 (mmp) REVERT: 4 111 GLN cc_start: 0.7203 (mt0) cc_final: 0.6805 (mt0) REVERT: 5 193 MET cc_start: 0.8241 (ttm) cc_final: 0.7464 (ttm) REVERT: 5 294 MET cc_start: 0.8646 (mmm) cc_final: 0.8229 (mmp) REVERT: 6 88 MET cc_start: 0.7397 (mtt) cc_final: 0.6975 (mtt) REVERT: 7 193 MET cc_start: 0.7896 (ttm) cc_final: 0.7587 (ttm) REVERT: 7 248 ILE cc_start: 0.9006 (mt) cc_final: 0.8708 (mt) REVERT: 9 175 SER cc_start: 0.8243 (p) cc_final: 0.7899 (t) REVERT: 9 176 LEU cc_start: 0.8521 (mt) cc_final: 0.8164 (mm) REVERT: 9 248 ILE cc_start: 0.8721 (mt) cc_final: 0.8519 (mt) REVERT: A 294 MET cc_start: 0.8615 (mmm) cc_final: 0.8262 (mmp) REVERT: A 350 TRP cc_start: 0.8373 (m100) cc_final: 0.8059 (m100) REVERT: B 24 LEU cc_start: 0.9187 (mt) cc_final: 0.8874 (mt) REVERT: B 34 GLU cc_start: 0.7481 (tp30) cc_final: 0.7245 (tp30) REVERT: B 88 MET cc_start: 0.7980 (mtt) cc_final: 0.7755 (mtm) REVERT: B 135 ASP cc_start: 0.6400 (p0) cc_final: 0.5938 (t0) REVERT: B 190 ARG cc_start: 0.7618 (ptt90) cc_final: 0.5461 (ptt-90) REVERT: C 279 LEU cc_start: 0.8754 (mt) cc_final: 0.8451 (mm) REVERT: C 350 TRP cc_start: 0.8301 (m100) cc_final: 0.7957 (m100) REVERT: D 24 LEU cc_start: 0.9214 (mt) cc_final: 0.8903 (mp) REVERT: F 88 MET cc_start: 0.8261 (mtt) cc_final: 0.7968 (mtt) REVERT: F 195 LEU cc_start: 0.9102 (mt) cc_final: 0.8875 (mt) REVERT: G 294 MET cc_start: 0.9105 (mmm) cc_final: 0.8843 (mmp) REVERT: H 40 GLN cc_start: 0.8029 (mt0) cc_final: 0.7781 (mt0) REVERT: J 40 GLN cc_start: 0.8221 (mt0) cc_final: 0.7793 (mt0) REVERT: J 88 MET cc_start: 0.7992 (mtt) cc_final: 0.7707 (mtt) REVERT: J 172 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7444 (tptp) REVERT: M 193 MET cc_start: 0.6932 (ttm) cc_final: 0.6601 (ttm) REVERT: M 294 MET cc_start: 0.9156 (mmm) cc_final: 0.8807 (mmm) REVERT: N 24 LEU cc_start: 0.9073 (mt) cc_final: 0.8868 (mt) REVERT: O 193 MET cc_start: 0.7121 (ttm) cc_final: 0.6783 (ttm) REVERT: O 350 TRP cc_start: 0.8019 (m100) cc_final: 0.7591 (m100) REVERT: P 111 GLN cc_start: 0.6999 (mt0) cc_final: 0.6723 (mt0) REVERT: R 138 GLU cc_start: 0.6228 (tt0) cc_final: 0.5921 (mp0) REVERT: S 173 LEU cc_start: 0.8973 (tp) cc_final: 0.8738 (tp) REVERT: S 294 MET cc_start: 0.9159 (mmm) cc_final: 0.8882 (mmp) REVERT: T 83 VAL cc_start: 0.8765 (t) cc_final: 0.8403 (p) REVERT: T 111 GLN cc_start: 0.8104 (mt0) cc_final: 0.7697 (mt0) REVERT: T 189 GLU cc_start: 0.8156 (pt0) cc_final: 0.7802 (pm20) REVERT: W 294 MET cc_start: 0.8733 (mmm) cc_final: 0.8494 (mmp) REVERT: W 359 ILE cc_start: 0.8315 (mt) cc_final: 0.7711 (mt) REVERT: X 111 GLN cc_start: 0.7704 (mt0) cc_final: 0.7364 (mt0) REVERT: Y 294 MET cc_start: 0.8876 (mmm) cc_final: 0.8342 (mmp) REVERT: Y 350 TRP cc_start: 0.8268 (m100) cc_final: 0.7981 (m100) REVERT: b 294 MET cc_start: 0.8129 (mmm) cc_final: 0.7415 (mmp) REVERT: d 248 ILE cc_start: 0.9039 (mt) cc_final: 0.8586 (mt) REVERT: d 279 LEU cc_start: 0.8896 (mt) cc_final: 0.8478 (mt) REVERT: e 111 GLN cc_start: 0.7292 (mt0) cc_final: 0.7061 (mt0) REVERT: e 163 GLN cc_start: 0.8354 (mt0) cc_final: 0.8003 (tp40) REVERT: f 294 MET cc_start: 0.8035 (mmm) cc_final: 0.7526 (mmp) REVERT: g 101 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6936 (mt-10) REVERT: g 111 GLN cc_start: 0.7052 (mt0) cc_final: 0.6810 (mt0) REVERT: g 154 TYR cc_start: 0.7995 (m-80) cc_final: 0.7783 (m-80) REVERT: h 193 MET cc_start: 0.8326 (ttm) cc_final: 0.7714 (ttp) REVERT: h 294 MET cc_start: 0.8556 (mmm) cc_final: 0.8241 (mmp) REVERT: i 82 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7287 (ttm-80) REVERT: k 111 GLN cc_start: 0.7421 (mt0) cc_final: 0.7067 (mt0) REVERT: l 175 SER cc_start: 0.7841 (p) cc_final: 0.7289 (t) REVERT: l 181 LYS cc_start: 0.6730 (pttp) cc_final: 0.6399 (pttt) REVERT: l 193 MET cc_start: 0.8219 (ttm) cc_final: 0.7884 (ttm) REVERT: l 294 MET cc_start: 0.8290 (mmm) cc_final: 0.7975 (mmp) outliers start: 0 outliers final: 0 residues processed: 1526 average time/residue: 0.8525 time to fit residues: 2045.9205 Evaluate side-chains 631 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 6.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 1.9990 chunk 673 optimal weight: 4.9990 chunk 373 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 454 optimal weight: 8.9990 chunk 359 optimal weight: 0.0670 chunk 696 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 423 optimal weight: 0.8980 chunk 518 optimal weight: 0.0980 chunk 806 optimal weight: 10.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 111 GLN 0 163 GLN 0 173 ASN 2 173 ASN ** 2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 76 GLN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 139 ASN B 163 GLN B 173 ASN D 163 GLN D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN J 163 GLN J 173 ASN L 31 GLN L 163 GLN ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 40 GLN N 139 ASN N 163 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN P 163 GLN ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN R 40 GLN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN T 173 ASN V 163 GLN V 173 ASN X 173 ASN Z 139 ASN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 196 GLN f 219 ASN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 173 ASN k 118 GLN k 163 GLN ** k 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 74328 Z= 0.188 Angle : 0.581 9.105 100632 Z= 0.316 Chirality : 0.043 0.169 10944 Planarity : 0.005 0.046 13248 Dihedral : 3.924 22.911 10128 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.04 % Favored : 97.69 % Rotamer: Outliers : 0.01 % Allowed : 1.53 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.37 (0.09), residues: 8976 helix: 0.88 (0.08), residues: 3888 sheet: -0.09 (0.12), residues: 2184 loop : -0.12 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 350 HIS 0.005 0.001 HIS 4 147 PHE 0.014 0.002 PHE 4 175 TYR 0.013 0.001 TYR O 346 ARG 0.018 0.001 ARG 5 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 962 time to evaluate : 6.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 181 ASP cc_start: 0.6596 (t0) cc_final: 0.6261 (t0) REVERT: 0 203 LYS cc_start: 0.7247 (pptt) cc_final: 0.6795 (pptt) REVERT: 1 250 PHE cc_start: 0.7748 (m-80) cc_final: 0.7500 (m-80) REVERT: 1 294 MET cc_start: 0.8190 (mmm) cc_final: 0.7461 (mmp) REVERT: 2 25 LYS cc_start: 0.7087 (mmtm) cc_final: 0.6620 (mmtm) REVERT: 2 118 GLN cc_start: 0.7794 (pt0) cc_final: 0.7529 (tt0) REVERT: 3 196 VAL cc_start: 0.8676 (t) cc_final: 0.8306 (m) REVERT: 5 175 SER cc_start: 0.7973 (t) cc_final: 0.7719 (t) REVERT: 5 193 MET cc_start: 0.7813 (ttm) cc_final: 0.7468 (ttp) REVERT: 5 294 MET cc_start: 0.8231 (mmm) cc_final: 0.7804 (mmp) REVERT: 6 88 MET cc_start: 0.7503 (mtt) cc_final: 0.7132 (mtt) REVERT: 7 193 MET cc_start: 0.7661 (ttm) cc_final: 0.7252 (ttm) REVERT: 9 175 SER cc_start: 0.8199 (p) cc_final: 0.7580 (t) REVERT: 9 219 ASN cc_start: 0.7174 (m-40) cc_final: 0.6971 (m-40) REVERT: A 324 THR cc_start: 0.9087 (p) cc_final: 0.8824 (t) REVERT: B 88 MET cc_start: 0.7870 (mtt) cc_final: 0.7608 (mtm) REVERT: C 350 TRP cc_start: 0.8472 (m100) cc_final: 0.8117 (m100) REVERT: D 34 GLU cc_start: 0.7593 (tp30) cc_final: 0.7385 (tp30) REVERT: D 203 LYS cc_start: 0.8111 (pptt) cc_final: 0.7860 (pptt) REVERT: E 294 MET cc_start: 0.8662 (mmp) cc_final: 0.8169 (mmp) REVERT: F 73 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8675 (ttpt) REVERT: F 88 MET cc_start: 0.8125 (mtt) cc_final: 0.7872 (mtt) REVERT: F 141 ARG cc_start: 0.7390 (mmt90) cc_final: 0.7045 (mtt90) REVERT: G 193 MET cc_start: 0.7618 (ttp) cc_final: 0.6733 (ptm) REVERT: H 83 VAL cc_start: 0.8768 (t) cc_final: 0.8514 (p) REVERT: J 88 MET cc_start: 0.7787 (mtt) cc_final: 0.7547 (mtt) REVERT: J 118 GLN cc_start: 0.7163 (tt0) cc_final: 0.6947 (tt0) REVERT: K 232 ILE cc_start: 0.8956 (mt) cc_final: 0.8689 (mt) REVERT: L 181 ASP cc_start: 0.6568 (t0) cc_final: 0.6154 (t0) REVERT: M 229 ASN cc_start: 0.7580 (t0) cc_final: 0.6969 (t0) REVERT: N 24 LEU cc_start: 0.8944 (mt) cc_final: 0.8718 (mp) REVERT: N 191 SER cc_start: 0.8479 (p) cc_final: 0.8197 (m) REVERT: O 229 ASN cc_start: 0.7739 (t0) cc_final: 0.7210 (t0) REVERT: O 350 TRP cc_start: 0.8097 (m100) cc_final: 0.7723 (m100) REVERT: P 141 ARG cc_start: 0.7009 (mtt90) cc_final: 0.6353 (ttm110) REVERT: P 181 ASP cc_start: 0.6678 (t0) cc_final: 0.6442 (t0) REVERT: Q 294 MET cc_start: 0.8878 (mmp) cc_final: 0.8224 (mmp) REVERT: R 141 ARG cc_start: 0.7515 (mmt90) cc_final: 0.6418 (mtt-85) REVERT: S 173 LEU cc_start: 0.8892 (tp) cc_final: 0.8609 (tp) REVERT: S 193 MET cc_start: 0.7263 (ttm) cc_final: 0.7019 (ttp) REVERT: T 203 LYS cc_start: 0.6930 (pptt) cc_final: 0.6539 (pptt) REVERT: V 83 VAL cc_start: 0.8643 (t) cc_final: 0.8388 (p) REVERT: W 193 MET cc_start: 0.8005 (ttp) cc_final: 0.6935 (ptm) REVERT: X 25 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6539 (ttmt) REVERT: X 203 LYS cc_start: 0.7225 (pptt) cc_final: 0.6140 (tptp) REVERT: Y 294 MET cc_start: 0.8724 (mmm) cc_final: 0.8175 (mmp) REVERT: Z 144 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7962 (mtmm) REVERT: b 324 THR cc_start: 0.9111 (p) cc_final: 0.8799 (t) REVERT: c 144 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7969 (mtmm) REVERT: d 193 MET cc_start: 0.7523 (ttp) cc_final: 0.6094 (ptm) REVERT: d 294 MET cc_start: 0.7960 (mmm) cc_final: 0.7063 (mmp) REVERT: e 163 GLN cc_start: 0.8743 (mt0) cc_final: 0.8088 (mt0) REVERT: e 203 LYS cc_start: 0.7461 (pptt) cc_final: 0.6918 (pptt) REVERT: g 179 ASP cc_start: 0.7656 (p0) cc_final: 0.7261 (m-30) REVERT: h 193 MET cc_start: 0.8172 (ttm) cc_final: 0.7842 (ttp) REVERT: h 294 MET cc_start: 0.8111 (mmm) cc_final: 0.7692 (mmp) REVERT: i 34 GLU cc_start: 0.7815 (tp30) cc_final: 0.7537 (tp30) REVERT: l 175 SER cc_start: 0.7827 (p) cc_final: 0.7409 (t) REVERT: l 294 MET cc_start: 0.8048 (mmm) cc_final: 0.7479 (mmp) outliers start: 1 outliers final: 0 residues processed: 963 average time/residue: 0.7784 time to fit residues: 1221.0146 Evaluate side-chains 564 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 6.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 671 optimal weight: 0.0000 chunk 549 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 807 optimal weight: 0.0980 chunk 872 optimal weight: 0.9990 chunk 719 optimal weight: 8.9990 chunk 801 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 648 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 219 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 ASN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 74328 Z= 0.164 Angle : 0.509 9.575 100632 Z= 0.268 Chirality : 0.041 0.174 10944 Planarity : 0.004 0.048 13248 Dihedral : 3.857 21.836 10128 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.11 % Favored : 97.63 % Rotamer: Outliers : 0.01 % Allowed : 1.39 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.00 (0.09), residues: 8976 helix: 1.51 (0.08), residues: 3864 sheet: 0.13 (0.11), residues: 2184 loop : 0.12 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 350 HIS 0.007 0.001 HIS 7 249 PHE 0.018 0.001 PHE f 258 TYR 0.011 0.001 TYR Z 154 ARG 0.017 0.000 ARG a 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 818 time to evaluate : 6.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 181 ASP cc_start: 0.6752 (t0) cc_final: 0.6302 (t0) REVERT: 0 203 LYS cc_start: 0.7470 (pptt) cc_final: 0.7012 (pptt) REVERT: 1 193 MET cc_start: 0.8071 (ttm) cc_final: 0.7547 (ttm) REVERT: 1 294 MET cc_start: 0.8145 (mmm) cc_final: 0.7377 (mmp) REVERT: 2 25 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6964 (mmtm) REVERT: 5 193 MET cc_start: 0.8052 (ttm) cc_final: 0.7701 (ttp) REVERT: 5 294 MET cc_start: 0.8200 (mmm) cc_final: 0.7677 (mmt) REVERT: 6 41 MET cc_start: 0.7115 (tmm) cc_final: 0.6840 (tmm) REVERT: 6 88 MET cc_start: 0.7431 (mtt) cc_final: 0.6897 (mtt) REVERT: 7 193 MET cc_start: 0.7741 (ttm) cc_final: 0.7384 (ttm) REVERT: 8 155 GLU cc_start: 0.7296 (pp20) cc_final: 0.7008 (tm-30) REVERT: 8 163 GLN cc_start: 0.8056 (mm110) cc_final: 0.7523 (mm-40) REVERT: 9 175 SER cc_start: 0.8332 (p) cc_final: 0.7919 (t) REVERT: 9 193 MET cc_start: 0.7790 (ttp) cc_final: 0.6280 (ptm) REVERT: 9 294 MET cc_start: 0.7489 (mmm) cc_final: 0.6505 (mtp) REVERT: A 181 LYS cc_start: 0.6419 (pttp) cc_final: 0.6210 (pttm) REVERT: A 324 THR cc_start: 0.9059 (p) cc_final: 0.8815 (t) REVERT: C 350 TRP cc_start: 0.8454 (m100) cc_final: 0.8202 (m100) REVERT: D 34 GLU cc_start: 0.7403 (tp30) cc_final: 0.7167 (tp30) REVERT: F 73 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8496 (ttpt) REVERT: F 203 LYS cc_start: 0.7242 (pptt) cc_final: 0.6996 (pptt) REVERT: G 193 MET cc_start: 0.7958 (ttp) cc_final: 0.7245 (ttm) REVERT: G 283 MET cc_start: 0.5970 (mpp) cc_final: 0.5769 (mpp) REVERT: H 73 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8696 (ttpp) REVERT: H 88 MET cc_start: 0.7883 (mtt) cc_final: 0.7659 (mtt) REVERT: J 34 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7309 (mm-30) REVERT: K 200 ASN cc_start: 0.9026 (t0) cc_final: 0.8814 (t0) REVERT: K 232 ILE cc_start: 0.8856 (mt) cc_final: 0.8649 (mt) REVERT: L 181 ASP cc_start: 0.6481 (t0) cc_final: 0.6133 (t0) REVERT: M 294 MET cc_start: 0.8596 (mmp) cc_final: 0.8328 (mmm) REVERT: O 173 LEU cc_start: 0.8954 (tp) cc_final: 0.8705 (mt) REVERT: O 193 MET cc_start: 0.7011 (ttp) cc_final: 0.5602 (ptm) REVERT: O 229 ASN cc_start: 0.7769 (t0) cc_final: 0.7338 (t0) REVERT: O 350 TRP cc_start: 0.8287 (m100) cc_final: 0.7870 (m100) REVERT: P 141 ARG cc_start: 0.6968 (mtt90) cc_final: 0.5844 (ttm110) REVERT: S 294 MET cc_start: 0.8749 (mmp) cc_final: 0.8482 (mmp) REVERT: T 84 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6214 (mt-10) REVERT: W 205 LEU cc_start: 0.9257 (mt) cc_final: 0.8956 (mm) REVERT: W 359 ILE cc_start: 0.8240 (mt) cc_final: 0.7862 (mt) REVERT: X 25 LYS cc_start: 0.7341 (ttmm) cc_final: 0.6947 (ttmt) REVERT: X 120 MET cc_start: 0.8511 (mtp) cc_final: 0.8128 (tpp) REVERT: X 154 TYR cc_start: 0.8249 (m-80) cc_final: 0.7973 (m-10) REVERT: X 203 LYS cc_start: 0.7093 (pptt) cc_final: 0.6131 (tptp) REVERT: Y 294 MET cc_start: 0.8560 (mmm) cc_final: 0.8141 (mmp) REVERT: Z 102 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7948 (mmtm) REVERT: Z 144 LYS cc_start: 0.8522 (mmpt) cc_final: 0.8028 (mtmm) REVERT: Z 154 TYR cc_start: 0.7437 (m-80) cc_final: 0.7147 (m-80) REVERT: a 118 GLN cc_start: 0.7327 (tt0) cc_final: 0.7068 (tt0) REVERT: a 163 GLN cc_start: 0.7880 (mm110) cc_final: 0.7305 (mm110) REVERT: b 294 MET cc_start: 0.8215 (mmt) cc_final: 0.7171 (mmp) REVERT: b 324 THR cc_start: 0.9187 (p) cc_final: 0.8941 (t) REVERT: c 144 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8343 (mtmm) REVERT: d 250 PHE cc_start: 0.7664 (m-80) cc_final: 0.7341 (m-80) REVERT: d 294 MET cc_start: 0.8025 (mmm) cc_final: 0.7095 (mmp) REVERT: e 141 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6582 (mmm160) REVERT: e 163 GLN cc_start: 0.8560 (mt0) cc_final: 0.8089 (mt0) REVERT: e 200 THR cc_start: 0.8511 (p) cc_final: 0.8265 (t) REVERT: e 203 LYS cc_start: 0.7243 (pptt) cc_final: 0.6634 (pptt) REVERT: h 175 SER cc_start: 0.8791 (p) cc_final: 0.8349 (p) REVERT: h 193 MET cc_start: 0.8348 (ttm) cc_final: 0.7913 (ttp) REVERT: i 34 GLU cc_start: 0.7881 (tp30) cc_final: 0.7548 (tp30) REVERT: k 34 GLU cc_start: 0.7720 (tp30) cc_final: 0.7486 (mm-30) REVERT: k 56 TYR cc_start: 0.8867 (m-80) cc_final: 0.8372 (m-80) REVERT: k 154 TYR cc_start: 0.7679 (m-80) cc_final: 0.7059 (m-80) REVERT: k 203 LYS cc_start: 0.7922 (pptt) cc_final: 0.7601 (pptt) REVERT: l 175 SER cc_start: 0.7769 (p) cc_final: 0.7278 (t) REVERT: l 193 MET cc_start: 0.8848 (ttp) cc_final: 0.7887 (ptm) REVERT: l 232 ILE cc_start: 0.9152 (mm) cc_final: 0.8861 (mt) outliers start: 1 outliers final: 0 residues processed: 818 average time/residue: 0.8119 time to fit residues: 1063.2988 Evaluate side-chains 546 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 6.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 3.9990 chunk 607 optimal weight: 10.0000 chunk 419 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 385 optimal weight: 0.9990 chunk 542 optimal weight: 1.9990 chunk 810 optimal weight: 5.9990 chunk 858 optimal weight: 9.9990 chunk 423 optimal weight: 8.9990 chunk 768 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 249 HIS ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS D 173 ASN F 173 ASN H 163 GLN H 173 ASN J 118 GLN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 173 ASN N 162 HIS ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 HIS P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 173 ASN U 219 ASN U 249 HIS V 111 GLN V 173 ASN W 249 HIS ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 111 GLN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 162 HIS i 173 ASN l 249 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 74328 Z= 0.290 Angle : 0.560 8.782 100632 Z= 0.291 Chirality : 0.043 0.169 10944 Planarity : 0.004 0.077 13248 Dihedral : 3.971 15.764 10128 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.79 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.21 (0.09), residues: 8976 helix: 1.77 (0.08), residues: 3720 sheet: 0.31 (0.11), residues: 2136 loop : 0.11 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 259 HIS 0.006 0.001 HIS B 42 PHE 0.017 0.002 PHE F 65 TYR 0.016 0.001 TYR 2 154 ARG 0.009 0.001 ARG N 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 7.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 181 ASP cc_start: 0.7077 (t0) cc_final: 0.6540 (t0) REVERT: 1 219 ASN cc_start: 0.6816 (p0) cc_final: 0.5775 (p0) REVERT: 1 294 MET cc_start: 0.8153 (mmm) cc_final: 0.7546 (mmp) REVERT: 2 25 LYS cc_start: 0.7618 (mmtm) cc_final: 0.7330 (mmtm) REVERT: 2 141 ARG cc_start: 0.6765 (mmm-85) cc_final: 0.6245 (mmm160) REVERT: 3 193 MET cc_start: 0.8580 (ttp) cc_final: 0.8240 (ttp) REVERT: 5 193 MET cc_start: 0.8235 (ttm) cc_final: 0.7866 (ttp) REVERT: 6 41 MET cc_start: 0.7776 (tmm) cc_final: 0.6969 (tmm) REVERT: 6 88 MET cc_start: 0.7521 (mtt) cc_final: 0.6925 (mtt) REVERT: 8 155 GLU cc_start: 0.7779 (pp20) cc_final: 0.7380 (tm-30) REVERT: 8 167 ILE cc_start: 0.9224 (mp) cc_final: 0.9010 (mt) REVERT: 9 175 SER cc_start: 0.7610 (p) cc_final: 0.7274 (t) REVERT: 9 193 MET cc_start: 0.7846 (ttp) cc_final: 0.7054 (ptm) REVERT: 9 294 MET cc_start: 0.7508 (mmm) cc_final: 0.6858 (mmm) REVERT: A 324 THR cc_start: 0.9079 (p) cc_final: 0.8841 (t) REVERT: B 41 MET cc_start: 0.7901 (tmm) cc_final: 0.7606 (tmm) REVERT: C 193 MET cc_start: 0.8306 (ttp) cc_final: 0.7262 (ptm) REVERT: C 267 MET cc_start: 0.7200 (tpp) cc_final: 0.6606 (tpt) REVERT: F 73 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8728 (ttpt) REVERT: F 88 MET cc_start: 0.8334 (mtp) cc_final: 0.8006 (mtt) REVERT: F 173 ASN cc_start: 0.8628 (m110) cc_final: 0.8321 (t0) REVERT: F 203 LYS cc_start: 0.7317 (pptt) cc_final: 0.6984 (pptt) REVERT: G 193 MET cc_start: 0.7901 (ttp) cc_final: 0.7463 (ttp) REVERT: H 88 MET cc_start: 0.7896 (mtt) cc_final: 0.7506 (mtt) REVERT: J 118 GLN cc_start: 0.7833 (tt0) cc_final: 0.7460 (tt0) REVERT: K 193 MET cc_start: 0.7008 (ttt) cc_final: 0.6659 (ttt) REVERT: L 181 ASP cc_start: 0.6908 (t0) cc_final: 0.6533 (t0) REVERT: P 203 LYS cc_start: 0.7396 (pptt) cc_final: 0.7129 (pptt) REVERT: R 25 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8248 (tttp) REVERT: T 88 MET cc_start: 0.7685 (mtt) cc_final: 0.7284 (mtt) REVERT: W 294 MET cc_start: 0.8165 (mmp) cc_final: 0.7647 (mmm) REVERT: X 25 LYS cc_start: 0.7565 (ttmm) cc_final: 0.7341 (ttmt) REVERT: X 203 LYS cc_start: 0.7018 (pptt) cc_final: 0.5946 (tptp) REVERT: Y 294 MET cc_start: 0.8589 (mmm) cc_final: 0.8318 (mmm) REVERT: Z 41 MET cc_start: 0.7799 (tmm) cc_final: 0.7453 (tmm) REVERT: Z 144 LYS cc_start: 0.8697 (mmpt) cc_final: 0.8323 (mtmm) REVERT: a 41 MET cc_start: 0.7546 (tmm) cc_final: 0.6510 (tmm) REVERT: a 118 GLN cc_start: 0.7337 (tt0) cc_final: 0.7029 (tt0) REVERT: a 154 TYR cc_start: 0.8021 (m-80) cc_final: 0.7527 (m-80) REVERT: b 294 MET cc_start: 0.8100 (mmt) cc_final: 0.7506 (mmp) REVERT: b 324 THR cc_start: 0.9168 (p) cc_final: 0.8934 (t) REVERT: c 25 LYS cc_start: 0.8373 (mttm) cc_final: 0.8096 (mptt) REVERT: c 104 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7881 (mtm180) REVERT: c 200 THR cc_start: 0.9366 (p) cc_final: 0.9047 (t) REVERT: d 294 MET cc_start: 0.8252 (mmm) cc_final: 0.7338 (mmp) REVERT: e 163 GLN cc_start: 0.8583 (mt0) cc_final: 0.8275 (mt0) REVERT: e 200 THR cc_start: 0.8381 (p) cc_final: 0.8047 (t) REVERT: e 203 LYS cc_start: 0.7509 (pptt) cc_final: 0.6978 (pptt) REVERT: f 193 MET cc_start: 0.8139 (ttt) cc_final: 0.7481 (ttm) REVERT: g 203 LYS cc_start: 0.6045 (pptt) cc_final: 0.5814 (pptt) REVERT: h 175 SER cc_start: 0.8709 (p) cc_final: 0.8273 (p) REVERT: h 193 MET cc_start: 0.8389 (ttm) cc_final: 0.8061 (ttp) REVERT: i 34 GLU cc_start: 0.7919 (tp30) cc_final: 0.7601 (tp30) REVERT: k 203 LYS cc_start: 0.7797 (pptt) cc_final: 0.7367 (pptt) REVERT: l 175 SER cc_start: 0.8122 (p) cc_final: 0.7828 (t) REVERT: l 193 MET cc_start: 0.8400 (ttp) cc_final: 0.7624 (ptm) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.7992 time to fit residues: 858.8166 Evaluate side-chains 494 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 6.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 2.9990 chunk 487 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 639 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 chunk 732 optimal weight: 10.0000 chunk 593 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 438 optimal weight: 5.9990 chunk 770 optimal weight: 9.9990 chunk 216 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 162 HIS ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 162 HIS ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 162 HIS ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 HIS D 173 ASN F 111 GLN F 162 HIS H 162 HIS H 173 ASN I 219 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS N 173 ASN P 162 HIS P 173 ASN R 162 HIS R 173 ASN T 162 HIS T 173 ASN U 219 ASN V 162 HIS W 219 ASN X 162 HIS ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 219 ASN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 40 GLN g 162 HIS ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN k 173 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 74328 Z= 0.232 Angle : 0.516 8.370 100632 Z= 0.268 Chirality : 0.042 0.175 10944 Planarity : 0.004 0.038 13248 Dihedral : 3.944 18.456 10128 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.72 % Favored : 97.01 % Rotamer: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.37 (0.09), residues: 8976 helix: 2.00 (0.08), residues: 3696 sheet: 0.38 (0.11), residues: 2136 loop : 0.09 (0.10), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 206 HIS 0.004 0.001 HIS 3 249 PHE 0.019 0.001 PHE 9 258 TYR 0.011 0.001 TYR A 216 ARG 0.007 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 638 time to evaluate : 6.671 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: 0 118 GLN cc_start: 0.7579 (tt0) cc_final: 0.7313 (tt0) REVERT: 0 181 ASP cc_start: 0.7043 (t0) cc_final: 0.6546 (t0) REVERT: 1 193 MET cc_start: 0.8365 (tpp) cc_final: 0.7557 (tpp) REVERT: 1 219 ASN cc_start: 0.6406 (p0) cc_final: 0.5867 (p0) REVERT: 1 294 MET cc_start: 0.8058 (mmm) cc_final: 0.7540 (mmp) REVERT: 4 139 ASN cc_start: 0.4361 (t0) cc_final: 0.4156 (t0) REVERT: 6 41 MET cc_start: 0.8058 (tmm) cc_final: 0.6985 (tmm) REVERT: 8 155 GLU cc_start: 0.7856 (pp20) cc_final: 0.7439 (tm-30) REVERT: 8 167 ILE cc_start: 0.9211 (mp) cc_final: 0.8982 (mt) REVERT: 9 175 SER cc_start: 0.7416 (p) cc_final: 0.7044 (t) REVERT: 9 193 MET cc_start: 0.8037 (ttp) cc_final: 0.7226 (ptm) REVERT: 9 294 MET cc_start: 0.7713 (mmm) cc_final: 0.7167 (mmm) REVERT: A 294 MET cc_start: 0.8350 (mmp) cc_final: 0.7979 (mmp) REVERT: A 324 THR cc_start: 0.9058 (p) cc_final: 0.8836 (t) REVERT: B 41 MET cc_start: 0.8241 (tmm) cc_final: 0.7698 (tmm) REVERT: C 193 MET cc_start: 0.8200 (ttp) cc_final: 0.7384 (ptm) REVERT: C 267 MET cc_start: 0.7280 (tpp) cc_final: 0.7025 (tpp) REVERT: F 25 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8243 (tttp) REVERT: F 154 TYR cc_start: 0.8537 (m-80) cc_final: 0.8319 (m-80) REVERT: G 193 MET cc_start: 0.7932 (ttp) cc_final: 0.7709 (ttp) REVERT: H 88 MET cc_start: 0.8006 (mtt) cc_final: 0.7514 (mtt) REVERT: J 40 GLN cc_start: 0.7800 (mt0) cc_final: 0.7437 (mt0) REVERT: L 181 ASP cc_start: 0.6880 (t0) cc_final: 0.6518 (t0) REVERT: P 25 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7827 (tmtt) REVERT: P 203 LYS cc_start: 0.7562 (pptt) cc_final: 0.7050 (pptt) REVERT: R 25 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8210 (tttp) REVERT: T 88 MET cc_start: 0.7873 (mtt) cc_final: 0.7659 (mtt) REVERT: W 193 MET cc_start: 0.8539 (ttp) cc_final: 0.6797 (ptm) REVERT: W 294 MET cc_start: 0.8106 (mmp) cc_final: 0.7625 (mmm) REVERT: X 25 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7368 (ttmt) REVERT: X 203 LYS cc_start: 0.6451 (pptt) cc_final: 0.5529 (tptp) REVERT: Y 193 MET cc_start: 0.8440 (ttp) cc_final: 0.8220 (ttp) REVERT: Y 294 MET cc_start: 0.8612 (mmm) cc_final: 0.8292 (mmm) REVERT: Z 25 LYS cc_start: 0.8436 (mttm) cc_final: 0.7883 (mptt) REVERT: Z 141 ARG cc_start: 0.6313 (mmm160) cc_final: 0.5925 (mtp85) REVERT: Z 144 LYS cc_start: 0.8638 (mmpt) cc_final: 0.8383 (mtmm) REVERT: a 41 MET cc_start: 0.8027 (tmm) cc_final: 0.6760 (tmm) REVERT: a 118 GLN cc_start: 0.7300 (tt0) cc_final: 0.7041 (tt0) REVERT: b 294 MET cc_start: 0.7846 (mmt) cc_final: 0.7476 (mmp) REVERT: b 324 THR cc_start: 0.9138 (p) cc_final: 0.8923 (t) REVERT: c 25 LYS cc_start: 0.8359 (mttm) cc_final: 0.8151 (mptt) REVERT: c 41 MET cc_start: 0.8304 (tmm) cc_final: 0.7868 (tmm) REVERT: c 144 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8440 (mtmm) REVERT: d 294 MET cc_start: 0.8073 (mmm) cc_final: 0.7411 (mmp) REVERT: e 163 GLN cc_start: 0.8464 (mt0) cc_final: 0.8134 (mt0) REVERT: e 200 THR cc_start: 0.8355 (p) cc_final: 0.8046 (t) REVERT: e 203 LYS cc_start: 0.7543 (pptt) cc_final: 0.6993 (pptt) REVERT: h 175 SER cc_start: 0.8657 (p) cc_final: 0.8270 (p) REVERT: h 193 MET cc_start: 0.8353 (ttm) cc_final: 0.8112 (ttp) REVERT: i 34 GLU cc_start: 0.7865 (tp30) cc_final: 0.7486 (tp30) REVERT: i 40 GLN cc_start: 0.8014 (pt0) cc_final: 0.7813 (pt0) REVERT: k 41 MET cc_start: 0.7833 (tmm) cc_final: 0.7542 (tmm) REVERT: l 175 SER cc_start: 0.8269 (p) cc_final: 0.8006 (t) REVERT: l 193 MET cc_start: 0.8612 (ttp) cc_final: 0.7871 (ptm) REVERT: l 283 MET cc_start: 0.6600 (mpp) cc_final: 0.6327 (mpp) outliers start: 2 outliers final: 0 residues processed: 640 average time/residue: 0.7799 time to fit residues: 811.0913 Evaluate side-chains 494 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 6.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 6.9990 chunk 772 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 503 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 859 optimal weight: 1.9990 chunk 713 optimal weight: 3.9990 chunk 397 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 284 optimal weight: 7.9990 chunk 451 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: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN 3 219 ASN 4 139 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 162 HIS ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN F 139 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 219 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 173 ASN ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 HIS ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 162 HIS g 139 ASN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 74328 Z= 0.169 Angle : 0.479 6.060 100632 Z= 0.247 Chirality : 0.041 0.216 10944 Planarity : 0.003 0.038 13248 Dihedral : 3.838 17.745 10128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.74 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.51 (0.09), residues: 8976 helix: 2.18 (0.08), residues: 3696 sheet: 0.46 (0.11), residues: 2136 loop : 0.06 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 206 HIS 0.003 0.001 HIS i 42 PHE 0.011 0.001 PHE 9 258 TYR 0.009 0.001 TYR 9 346 ARG 0.009 0.000 ARG 8 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 6.762 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: 0 118 GLN cc_start: 0.7565 (tt0) cc_final: 0.7247 (tt0) REVERT: 0 181 ASP cc_start: 0.7076 (t0) cc_final: 0.6515 (t0) REVERT: 1 193 MET cc_start: 0.8226 (tpp) cc_final: 0.7613 (tpp) REVERT: 1 219 ASN cc_start: 0.6308 (p0) cc_final: 0.5943 (p0) REVERT: 1 294 MET cc_start: 0.8020 (mmm) cc_final: 0.7514 (mmp) REVERT: 4 139 ASN cc_start: 0.4158 (t0) cc_final: 0.3915 (t0) REVERT: 4 203 LYS cc_start: 0.6272 (pptt) cc_final: 0.6058 (pptt) REVERT: 5 193 MET cc_start: 0.8349 (ttp) cc_final: 0.6859 (ptm) REVERT: 6 41 MET cc_start: 0.8126 (tmm) cc_final: 0.7041 (tmm) REVERT: 8 155 GLU cc_start: 0.7704 (pp20) cc_final: 0.7438 (tm-30) REVERT: 8 167 ILE cc_start: 0.9223 (mp) cc_final: 0.8932 (mt) REVERT: 9 175 SER cc_start: 0.7519 (p) cc_final: 0.7093 (t) REVERT: 9 294 MET cc_start: 0.7744 (mmm) cc_final: 0.7172 (mmm) REVERT: A 324 THR cc_start: 0.9082 (p) cc_final: 0.8841 (t) REVERT: B 41 MET cc_start: 0.8205 (tmm) cc_final: 0.7657 (tmm) REVERT: C 294 MET cc_start: 0.8218 (mmp) cc_final: 0.7950 (mmp) REVERT: F 25 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8304 (tttp) REVERT: F 118 GLN cc_start: 0.7646 (pt0) cc_final: 0.7422 (pt0) REVERT: F 154 TYR cc_start: 0.8527 (m-80) cc_final: 0.8141 (m-80) REVERT: F 163 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7554 (mm-40) REVERT: G 193 MET cc_start: 0.8087 (ttp) cc_final: 0.7824 (ttp) REVERT: H 88 MET cc_start: 0.7759 (mtt) cc_final: 0.7219 (mtt) REVERT: H 120 MET cc_start: 0.8198 (mtp) cc_final: 0.7806 (ttm) REVERT: J 40 GLN cc_start: 0.7648 (mt0) cc_final: 0.7279 (mt0) REVERT: L 181 ASP cc_start: 0.6902 (t0) cc_final: 0.6523 (t0) REVERT: M 193 MET cc_start: 0.7684 (ttp) cc_final: 0.7081 (tmm) REVERT: N 179 ASP cc_start: 0.8579 (p0) cc_final: 0.8293 (m-30) REVERT: O 193 MET cc_start: 0.7732 (tmm) cc_final: 0.7377 (ttp) REVERT: P 88 MET cc_start: 0.6624 (mtp) cc_final: 0.6378 (mtp) REVERT: P 203 LYS cc_start: 0.7413 (pptt) cc_final: 0.6852 (pptt) REVERT: R 25 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8215 (tttp) REVERT: T 88 MET cc_start: 0.7655 (mtt) cc_final: 0.7284 (mtt) REVERT: W 193 MET cc_start: 0.8555 (ttp) cc_final: 0.6963 (ptm) REVERT: X 203 LYS cc_start: 0.6563 (pptt) cc_final: 0.5543 (tptp) REVERT: Y 294 MET cc_start: 0.8552 (mmm) cc_final: 0.8266 (mmm) REVERT: Z 25 LYS cc_start: 0.8510 (mttm) cc_final: 0.7931 (mptt) REVERT: Z 41 MET cc_start: 0.7993 (tmm) cc_final: 0.7692 (tmm) REVERT: Z 141 ARG cc_start: 0.6436 (mmm160) cc_final: 0.6062 (mtp85) REVERT: Z 144 LYS cc_start: 0.8566 (mmpt) cc_final: 0.8317 (mtmm) REVERT: a 41 MET cc_start: 0.8209 (tmm) cc_final: 0.6867 (tmm) REVERT: b 294 MET cc_start: 0.7808 (mmt) cc_final: 0.7457 (mmp) REVERT: b 324 THR cc_start: 0.9248 (p) cc_final: 0.8967 (t) REVERT: c 25 LYS cc_start: 0.8651 (mttm) cc_final: 0.8226 (mptt) REVERT: c 41 MET cc_start: 0.8361 (tmm) cc_final: 0.7766 (tmm) REVERT: c 141 ARG cc_start: 0.6326 (mmm160) cc_final: 0.5807 (mtp85) REVERT: c 144 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8444 (mtmm) REVERT: d 294 MET cc_start: 0.8060 (mmm) cc_final: 0.7484 (mmm) REVERT: h 175 SER cc_start: 0.8664 (p) cc_final: 0.8277 (p) REVERT: h 193 MET cc_start: 0.8422 (ttm) cc_final: 0.8110 (ttp) REVERT: i 34 GLU cc_start: 0.7738 (tp30) cc_final: 0.7437 (tp30) REVERT: i 41 MET cc_start: 0.7908 (tmm) cc_final: 0.6917 (tmm) REVERT: i 144 LYS cc_start: 0.8808 (mppt) cc_final: 0.8538 (mtmm) REVERT: j 294 MET cc_start: 0.8381 (mtp) cc_final: 0.7855 (mtm) REVERT: k 34 GLU cc_start: 0.7765 (tp30) cc_final: 0.7563 (mm-30) REVERT: k 41 MET cc_start: 0.8013 (tmm) cc_final: 0.7696 (tmm) REVERT: l 175 SER cc_start: 0.8217 (p) cc_final: 0.7893 (t) REVERT: l 193 MET cc_start: 0.8533 (ttp) cc_final: 0.7880 (ptm) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.7755 time to fit residues: 784.1362 Evaluate side-chains 483 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 6.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 489 optimal weight: 4.9990 chunk 627 optimal weight: 0.0570 chunk 486 optimal weight: 0.9990 chunk 723 optimal weight: 6.9990 chunk 479 optimal weight: 2.9990 chunk 855 optimal weight: 8.9990 chunk 535 optimal weight: 5.9990 chunk 521 optimal weight: 0.1980 chunk 395 optimal weight: 3.9990 overall best weight: 1.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 219 ASN ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 111 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 219 ASN e 40 GLN g 139 ASN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN k 173 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 74328 Z= 0.177 Angle : 0.482 10.543 100632 Z= 0.247 Chirality : 0.041 0.176 10944 Planarity : 0.003 0.070 13248 Dihedral : 3.835 20.827 10128 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.80 % Favored : 96.94 % Rotamer: Outliers : 0.01 % Allowed : 0.53 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.59 (0.09), residues: 8976 helix: 2.27 (0.08), residues: 3696 sheet: 0.57 (0.11), residues: 2112 loop : 0.01 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 7 259 HIS 0.004 0.001 HIS 8 147 PHE 0.011 0.001 PHE 9 258 TYR 0.012 0.001 TYR Z 154 ARG 0.006 0.000 ARG J 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 603 time to evaluate : 8.513 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: 0 118 GLN cc_start: 0.7557 (tt0) cc_final: 0.7223 (tt0) REVERT: 0 181 ASP cc_start: 0.7030 (t0) cc_final: 0.6552 (t0) REVERT: 1 193 MET cc_start: 0.8363 (tpp) cc_final: 0.7695 (tpp) REVERT: 1 219 ASN cc_start: 0.6229 (p0) cc_final: 0.5893 (p0) REVERT: 1 294 MET cc_start: 0.8010 (mmm) cc_final: 0.7533 (mmp) REVERT: 4 139 ASN cc_start: 0.4485 (t0) cc_final: 0.4257 (t0) REVERT: 5 175 SER cc_start: 0.8538 (p) cc_final: 0.8108 (t) REVERT: 5 193 MET cc_start: 0.8339 (ttp) cc_final: 0.7390 (ptm) REVERT: 6 41 MET cc_start: 0.8334 (tmm) cc_final: 0.7383 (tmm) REVERT: 8 41 MET cc_start: 0.7954 (tmm) cc_final: 0.7615 (tmm) REVERT: 8 110 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7261 (tt0) REVERT: 9 175 SER cc_start: 0.7522 (p) cc_final: 0.7161 (t) REVERT: 9 193 MET cc_start: 0.8104 (ttp) cc_final: 0.6547 (ptm) REVERT: 9 294 MET cc_start: 0.7797 (mmm) cc_final: 0.7191 (mmm) REVERT: B 41 MET cc_start: 0.8183 (tmm) cc_final: 0.7582 (tmm) REVERT: B 141 ARG cc_start: 0.6802 (mmm160) cc_final: 0.6470 (mtp85) REVERT: C 294 MET cc_start: 0.8145 (mmp) cc_final: 0.7878 (mmp) REVERT: D 141 ARG cc_start: 0.6663 (mtt90) cc_final: 0.6430 (ttm110) REVERT: F 25 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8294 (tttp) REVERT: H 88 MET cc_start: 0.7859 (mtt) cc_final: 0.7564 (mtt) REVERT: H 120 MET cc_start: 0.8025 (mtp) cc_final: 0.7718 (ttm) REVERT: J 40 GLN cc_start: 0.7642 (mt0) cc_final: 0.7275 (mt0) REVERT: L 181 ASP cc_start: 0.6929 (t0) cc_final: 0.6476 (t0) REVERT: L 203 LYS cc_start: 0.7451 (pptt) cc_final: 0.7119 (pptt) REVERT: N 111 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5855 (mm110) REVERT: N 179 ASP cc_start: 0.8644 (p0) cc_final: 0.8263 (m-30) REVERT: P 203 LYS cc_start: 0.7237 (pptt) cc_final: 0.6670 (pptt) REVERT: S 193 MET cc_start: 0.7992 (ttm) cc_final: 0.7781 (mmm) REVERT: S 219 ASN cc_start: 0.6406 (m-40) cc_final: 0.6070 (m-40) REVERT: T 88 MET cc_start: 0.7688 (mtt) cc_final: 0.7346 (mtt) REVERT: W 193 MET cc_start: 0.8657 (ttp) cc_final: 0.6990 (ptm) REVERT: Y 294 MET cc_start: 0.8399 (mmm) cc_final: 0.8128 (mmm) REVERT: Z 41 MET cc_start: 0.8047 (tmm) cc_final: 0.7721 (tmm) REVERT: Z 141 ARG cc_start: 0.6428 (mmm160) cc_final: 0.6201 (mtp85) REVERT: Z 144 LYS cc_start: 0.8564 (mmpt) cc_final: 0.8267 (mtmm) REVERT: Z 167 ILE cc_start: 0.9335 (mp) cc_final: 0.8969 (mt) REVERT: a 41 MET cc_start: 0.8407 (tmm) cc_final: 0.7535 (tmm) REVERT: b 294 MET cc_start: 0.7877 (mmt) cc_final: 0.7674 (mmp) REVERT: c 25 LYS cc_start: 0.8658 (mttm) cc_final: 0.8261 (mptt) REVERT: c 41 MET cc_start: 0.8412 (tmm) cc_final: 0.7816 (tmm) REVERT: d 294 MET cc_start: 0.8068 (mmm) cc_final: 0.7519 (mmm) REVERT: e 203 LYS cc_start: 0.6638 (pptt) cc_final: 0.6395 (pptt) REVERT: g 25 LYS cc_start: 0.8754 (mptt) cc_final: 0.8412 (mptt) REVERT: h 175 SER cc_start: 0.8624 (p) cc_final: 0.8258 (p) REVERT: h 193 MET cc_start: 0.8422 (ttm) cc_final: 0.8092 (ttp) REVERT: i 34 GLU cc_start: 0.7753 (tp30) cc_final: 0.7407 (tp30) REVERT: i 41 MET cc_start: 0.8134 (tmm) cc_final: 0.7085 (tmm) REVERT: i 144 LYS cc_start: 0.8843 (mppt) cc_final: 0.8546 (mtmm) REVERT: k 41 MET cc_start: 0.8144 (tmm) cc_final: 0.7685 (tmm) REVERT: l 175 SER cc_start: 0.8189 (p) cc_final: 0.7882 (t) REVERT: l 193 MET cc_start: 0.8556 (ttp) cc_final: 0.7901 (ptm) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.7880 time to fit residues: 771.2231 Evaluate side-chains 479 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 6.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 511 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 544 optimal weight: 2.9990 chunk 583 optimal weight: 4.9990 chunk 423 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 672 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN 3 219 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 173 ASN ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 74328 Z= 0.149 Angle : 0.470 7.694 100632 Z= 0.241 Chirality : 0.041 0.160 10944 Planarity : 0.003 0.051 13248 Dihedral : 3.773 20.953 10128 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.66 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.67 (0.09), residues: 8976 helix: 2.30 (0.08), residues: 3720 sheet: 0.65 (0.11), residues: 2112 loop : 0.04 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 7 259 HIS 0.003 0.001 HIS H 147 PHE 0.010 0.001 PHE 9 258 TYR 0.011 0.001 TYR C 216 ARG 0.006 0.000 ARG g 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 6.741 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: 0 41 MET cc_start: 0.7875 (tmm) cc_final: 0.6929 (tmm) REVERT: 0 181 ASP cc_start: 0.6768 (t0) cc_final: 0.6262 (t0) REVERT: 1 193 MET cc_start: 0.8413 (tpp) cc_final: 0.7647 (tpp) REVERT: 1 219 ASN cc_start: 0.6434 (p0) cc_final: 0.5768 (p0) REVERT: 1 294 MET cc_start: 0.8009 (mmm) cc_final: 0.7536 (mmp) REVERT: 2 141 ARG cc_start: 0.6408 (mmm-85) cc_final: 0.6187 (mmm160) REVERT: 2 174 SER cc_start: 0.9065 (p) cc_final: 0.8864 (p) REVERT: 6 41 MET cc_start: 0.8207 (tmm) cc_final: 0.7286 (tmm) REVERT: 6 144 LYS cc_start: 0.8786 (mppt) cc_final: 0.8468 (mtmm) REVERT: 8 41 MET cc_start: 0.8028 (tmm) cc_final: 0.7656 (tmm) REVERT: 8 110 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7238 (tt0) REVERT: 9 175 SER cc_start: 0.7558 (p) cc_final: 0.7182 (t) REVERT: 9 193 MET cc_start: 0.8367 (ttp) cc_final: 0.6662 (ptm) REVERT: 9 294 MET cc_start: 0.7754 (mmm) cc_final: 0.7194 (mmp) REVERT: B 41 MET cc_start: 0.8515 (tmm) cc_final: 0.7999 (tmm) REVERT: B 141 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6469 (mtp85) REVERT: C 294 MET cc_start: 0.8107 (mmp) cc_final: 0.7842 (mmp) REVERT: D 141 ARG cc_start: 0.6474 (mtt90) cc_final: 0.6215 (ttm110) REVERT: F 25 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8325 (tttp) REVERT: F 141 ARG cc_start: 0.6495 (mtt-85) cc_final: 0.6073 (ttm110) REVERT: H 88 MET cc_start: 0.7801 (mtt) cc_final: 0.7492 (mtt) REVERT: J 40 GLN cc_start: 0.7754 (mt0) cc_final: 0.7419 (mt0) REVERT: J 163 GLN cc_start: 0.7783 (mm110) cc_final: 0.7443 (mm-40) REVERT: L 181 ASP cc_start: 0.6932 (t0) cc_final: 0.6474 (t0) REVERT: L 203 LYS cc_start: 0.7556 (pptt) cc_final: 0.7269 (pptt) REVERT: N 179 ASP cc_start: 0.8684 (p0) cc_final: 0.8279 (m-30) REVERT: P 203 LYS cc_start: 0.7413 (pptt) cc_final: 0.6695 (pptt) REVERT: T 88 MET cc_start: 0.7623 (mtt) cc_final: 0.7304 (mtt) REVERT: W 193 MET cc_start: 0.8695 (ttp) cc_final: 0.6962 (ptm) REVERT: Y 294 MET cc_start: 0.8387 (mmm) cc_final: 0.8066 (mmm) REVERT: Z 25 LYS cc_start: 0.8472 (mttm) cc_final: 0.7988 (mptt) REVERT: Z 41 MET cc_start: 0.8328 (tmm) cc_final: 0.8001 (tmm) REVERT: Z 144 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8278 (mtmm) REVERT: Z 167 ILE cc_start: 0.9301 (mp) cc_final: 0.8901 (mt) REVERT: a 41 MET cc_start: 0.8437 (tmm) cc_final: 0.7482 (tmm) REVERT: c 25 LYS cc_start: 0.8423 (mttm) cc_final: 0.8060 (mptt) REVERT: c 41 MET cc_start: 0.8567 (tmm) cc_final: 0.7985 (tmm) REVERT: c 141 ARG cc_start: 0.6099 (mmm160) cc_final: 0.5529 (mtp85) REVERT: d 294 MET cc_start: 0.8175 (mmm) cc_final: 0.7475 (mmm) REVERT: g 25 LYS cc_start: 0.8731 (mptt) cc_final: 0.8411 (mptt) REVERT: g 139 ASN cc_start: 0.5470 (t0) cc_final: 0.5117 (t0) REVERT: h 175 SER cc_start: 0.8644 (p) cc_final: 0.8248 (p) REVERT: h 193 MET cc_start: 0.8377 (ttm) cc_final: 0.8076 (ttp) REVERT: i 34 GLU cc_start: 0.7713 (tp30) cc_final: 0.7392 (tp30) REVERT: i 41 MET cc_start: 0.8195 (tmm) cc_final: 0.7078 (tmm) REVERT: k 41 MET cc_start: 0.8095 (tmm) cc_final: 0.7676 (tmm) REVERT: l 175 SER cc_start: 0.8087 (p) cc_final: 0.7780 (t) REVERT: l 193 MET cc_start: 0.8533 (ttp) cc_final: 0.7583 (ptm) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.7822 time to fit residues: 754.5963 Evaluate side-chains 483 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 1.9990 chunk 819 optimal weight: 0.0980 chunk 748 optimal weight: 5.9990 chunk 797 optimal weight: 3.9990 chunk 480 optimal weight: 5.9990 chunk 347 optimal weight: 0.0070 chunk 626 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 720 optimal weight: 6.9990 chunk 754 optimal weight: 5.9990 chunk 794 optimal weight: 9.9990 overall best weight: 2.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 249 HIS 2 173 ASN 3 219 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 249 HIS ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 173 ASN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN Q 249 HIS ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN ** k 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 74328 Z= 0.232 Angle : 0.509 7.956 100632 Z= 0.262 Chirality : 0.042 0.207 10944 Planarity : 0.003 0.046 13248 Dihedral : 3.883 22.140 10128 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 0.01 % Allowed : 0.21 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.58 (0.09), residues: 8976 helix: 2.24 (0.08), residues: 3720 sheet: 0.58 (0.11), residues: 2112 loop : 0.01 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 206 HIS 0.004 0.001 HIS L 147 PHE 0.013 0.001 PHE a 175 TYR 0.014 0.001 TYR C 216 ARG 0.006 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 569 time to evaluate : 7.101 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: 0 181 ASP cc_start: 0.6854 (t0) cc_final: 0.6401 (t0) REVERT: 1 193 MET cc_start: 0.8430 (tpp) cc_final: 0.7671 (tpp) REVERT: 1 219 ASN cc_start: 0.6541 (p0) cc_final: 0.5855 (p0) REVERT: 1 294 MET cc_start: 0.8003 (mmm) cc_final: 0.7657 (mmp) REVERT: 6 41 MET cc_start: 0.8390 (tmm) cc_final: 0.7413 (tmm) REVERT: 6 144 LYS cc_start: 0.8837 (mppt) cc_final: 0.8464 (mtmm) REVERT: 8 41 MET cc_start: 0.8198 (tmm) cc_final: 0.7591 (tmm) REVERT: 8 110 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7290 (tt0) REVERT: 9 175 SER cc_start: 0.7579 (p) cc_final: 0.7231 (t) REVERT: 9 193 MET cc_start: 0.8370 (ttp) cc_final: 0.6766 (ptm) REVERT: 9 294 MET cc_start: 0.7836 (mmm) cc_final: 0.7512 (mmm) REVERT: B 41 MET cc_start: 0.8214 (tmm) cc_final: 0.7682 (tmm) REVERT: B 141 ARG cc_start: 0.6843 (mmm160) cc_final: 0.6567 (mtp85) REVERT: C 193 MET cc_start: 0.7850 (ttp) cc_final: 0.7529 (tmm) REVERT: C 294 MET cc_start: 0.8126 (mmp) cc_final: 0.7841 (mmp) REVERT: D 141 ARG cc_start: 0.6537 (mtt90) cc_final: 0.6286 (ttm110) REVERT: D 144 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8726 (mtmt) REVERT: E 226 ASN cc_start: 0.8764 (m-40) cc_final: 0.8521 (m-40) REVERT: F 25 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8292 (tttp) REVERT: F 141 ARG cc_start: 0.6473 (mtt-85) cc_final: 0.6100 (ttm110) REVERT: H 88 MET cc_start: 0.7780 (mtt) cc_final: 0.7320 (mtt) REVERT: J 40 GLN cc_start: 0.7672 (mt0) cc_final: 0.7319 (mt0) REVERT: J 163 GLN cc_start: 0.7833 (mm110) cc_final: 0.7491 (mm-40) REVERT: L 181 ASP cc_start: 0.6914 (t0) cc_final: 0.6471 (t0) REVERT: N 41 MET cc_start: 0.8210 (tmm) cc_final: 0.7944 (tmm) REVERT: T 88 MET cc_start: 0.7728 (mtt) cc_final: 0.7385 (mtt) REVERT: T 181 ASP cc_start: 0.6779 (t0) cc_final: 0.6466 (t0) REVERT: V 41 MET cc_start: 0.8046 (tmm) cc_final: 0.7674 (tmm) REVERT: W 193 MET cc_start: 0.8730 (ttp) cc_final: 0.6891 (ptm) REVERT: Y 294 MET cc_start: 0.8337 (mmm) cc_final: 0.8104 (mmm) REVERT: Z 25 LYS cc_start: 0.8570 (mttm) cc_final: 0.8078 (mptt) REVERT: Z 41 MET cc_start: 0.8188 (tmm) cc_final: 0.7771 (tmm) REVERT: Z 167 ILE cc_start: 0.9284 (mp) cc_final: 0.8874 (mt) REVERT: a 41 MET cc_start: 0.8423 (tmm) cc_final: 0.7823 (tmm) REVERT: b 294 MET cc_start: 0.7702 (mmp) cc_final: 0.7479 (mmp) REVERT: c 25 LYS cc_start: 0.8674 (mttm) cc_final: 0.8299 (mptt) REVERT: c 41 MET cc_start: 0.8474 (tmm) cc_final: 0.7838 (tmm) REVERT: c 141 ARG cc_start: 0.6149 (mmm160) cc_final: 0.5600 (mtp85) REVERT: d 193 MET cc_start: 0.8385 (ttp) cc_final: 0.7869 (ttp) REVERT: d 294 MET cc_start: 0.8177 (mmm) cc_final: 0.7562 (mmm) REVERT: g 25 LYS cc_start: 0.8779 (mptt) cc_final: 0.8446 (mptt) REVERT: h 175 SER cc_start: 0.8595 (p) cc_final: 0.8219 (p) REVERT: h 193 MET cc_start: 0.8315 (ttm) cc_final: 0.8028 (ttp) REVERT: i 34 GLU cc_start: 0.7765 (tp30) cc_final: 0.7432 (tp30) REVERT: i 41 MET cc_start: 0.8226 (tmm) cc_final: 0.7345 (tmm) REVERT: i 144 LYS cc_start: 0.8883 (mppt) cc_final: 0.8545 (mtmm) REVERT: k 41 MET cc_start: 0.8177 (tmm) cc_final: 0.7617 (tmm) REVERT: l 175 SER cc_start: 0.8058 (p) cc_final: 0.7832 (t) outliers start: 1 outliers final: 0 residues processed: 570 average time/residue: 0.8310 time to fit residues: 770.0251 Evaluate side-chains 472 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 8.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 3.9990 chunk 843 optimal weight: 0.5980 chunk 514 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 586 optimal weight: 2.9990 chunk 884 optimal weight: 6.9990 chunk 814 optimal weight: 5.9990 chunk 704 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 544 optimal weight: 0.0470 chunk 431 optimal weight: 8.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN 3 219 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 173 ASN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN k 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 74328 Z= 0.168 Angle : 0.486 8.654 100632 Z= 0.249 Chirality : 0.041 0.207 10944 Planarity : 0.003 0.045 13248 Dihedral : 3.842 19.930 10128 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.64 (0.09), residues: 8976 helix: 2.30 (0.08), residues: 3720 sheet: 0.62 (0.11), residues: 2112 loop : 0.02 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP j 259 HIS 0.004 0.001 HIS 3 249 PHE 0.011 0.001 PHE f 258 TYR 0.012 0.001 TYR C 216 ARG 0.009 0.000 ARG 3 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 6.875 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: 0 181 ASP cc_start: 0.6720 (t0) cc_final: 0.6149 (t0) REVERT: 1 193 MET cc_start: 0.8422 (tpp) cc_final: 0.7634 (tpp) REVERT: 1 219 ASN cc_start: 0.6387 (p0) cc_final: 0.5824 (p0) REVERT: 2 174 SER cc_start: 0.9105 (p) cc_final: 0.8882 (p) REVERT: 5 193 MET cc_start: 0.8117 (ttp) cc_final: 0.7672 (ttp) REVERT: 6 41 MET cc_start: 0.8402 (tmm) cc_final: 0.7408 (tmm) REVERT: 6 144 LYS cc_start: 0.8832 (mppt) cc_final: 0.8514 (mtmm) REVERT: 6 154 TYR cc_start: 0.8289 (m-80) cc_final: 0.8029 (m-80) REVERT: 8 41 MET cc_start: 0.8234 (tmm) cc_final: 0.7758 (tmm) REVERT: 9 175 SER cc_start: 0.7578 (p) cc_final: 0.7225 (t) REVERT: 9 193 MET cc_start: 0.8150 (ttp) cc_final: 0.6711 (ptm) REVERT: 9 294 MET cc_start: 0.7804 (mmm) cc_final: 0.7525 (mmm) REVERT: B 41 MET cc_start: 0.8240 (tmm) cc_final: 0.7684 (tmm) REVERT: B 141 ARG cc_start: 0.6780 (mmm160) cc_final: 0.6541 (mtp85) REVERT: C 193 MET cc_start: 0.7843 (ttp) cc_final: 0.7538 (tmm) REVERT: C 294 MET cc_start: 0.8110 (mmp) cc_final: 0.7813 (mmp) REVERT: D 141 ARG cc_start: 0.6544 (mtt90) cc_final: 0.6212 (ttm110) REVERT: D 144 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8736 (mtmt) REVERT: E 226 ASN cc_start: 0.8750 (m-40) cc_final: 0.8529 (m-40) REVERT: F 141 ARG cc_start: 0.6432 (mtt-85) cc_final: 0.6072 (ttm110) REVERT: H 88 MET cc_start: 0.7887 (mtt) cc_final: 0.7591 (mtt) REVERT: I 193 MET cc_start: 0.7593 (tpp) cc_final: 0.7307 (mmm) REVERT: I 267 MET cc_start: 0.7532 (tpp) cc_final: 0.7261 (tpp) REVERT: J 25 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8174 (tttm) REVERT: J 40 GLN cc_start: 0.7781 (mt0) cc_final: 0.7444 (mt0) REVERT: J 163 GLN cc_start: 0.7766 (mm110) cc_final: 0.7471 (mm-40) REVERT: L 181 ASP cc_start: 0.6726 (t0) cc_final: 0.6295 (t0) REVERT: N 41 MET cc_start: 0.8258 (tmm) cc_final: 0.7982 (tmm) REVERT: P 41 MET cc_start: 0.8350 (tmm) cc_final: 0.7295 (tmm) REVERT: T 88 MET cc_start: 0.7504 (mtt) cc_final: 0.7152 (mtt) REVERT: T 181 ASP cc_start: 0.6852 (t0) cc_final: 0.6511 (t0) REVERT: V 41 MET cc_start: 0.8028 (tmm) cc_final: 0.7600 (tmm) REVERT: W 193 MET cc_start: 0.8741 (ttp) cc_final: 0.6886 (ptm) REVERT: Z 25 LYS cc_start: 0.8538 (mttm) cc_final: 0.8076 (mptt) REVERT: Z 41 MET cc_start: 0.8153 (tmm) cc_final: 0.7737 (tmm) REVERT: Z 167 ILE cc_start: 0.9224 (mp) cc_final: 0.8814 (mt) REVERT: a 41 MET cc_start: 0.8381 (tmm) cc_final: 0.7795 (tmm) REVERT: b 294 MET cc_start: 0.7760 (mmp) cc_final: 0.7523 (mmp) REVERT: c 25 LYS cc_start: 0.8454 (mttm) cc_final: 0.8082 (mptt) REVERT: c 41 MET cc_start: 0.8678 (tmm) cc_final: 0.8084 (tmm) REVERT: c 141 ARG cc_start: 0.6233 (mmm160) cc_final: 0.5681 (mtp85) REVERT: d 193 MET cc_start: 0.8369 (ttp) cc_final: 0.7870 (ttp) REVERT: d 294 MET cc_start: 0.8136 (mmm) cc_final: 0.7562 (mmm) REVERT: g 25 LYS cc_start: 0.8743 (mptt) cc_final: 0.8472 (mptt) REVERT: h 175 SER cc_start: 0.8600 (p) cc_final: 0.8215 (p) REVERT: h 193 MET cc_start: 0.8410 (ttm) cc_final: 0.8195 (ttp) REVERT: i 34 GLU cc_start: 0.7640 (tp30) cc_final: 0.7326 (tp30) REVERT: i 41 MET cc_start: 0.8176 (tmm) cc_final: 0.7243 (tmm) REVERT: k 41 MET cc_start: 0.8158 (tmm) cc_final: 0.7596 (tmm) REVERT: l 175 SER cc_start: 0.8055 (p) cc_final: 0.7822 (t) REVERT: l 193 MET cc_start: 0.8955 (ttp) cc_final: 0.8328 (ptm) outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.7756 time to fit residues: 712.7377 Evaluate side-chains 481 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 6.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 6.9990 chunk 750 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 649 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 705 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 162 HIS 2 173 ASN 7 249 HIS 8 139 ASN ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 173 ASN I 249 HIS ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 HIS ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 ASN S 249 HIS ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 249 HIS Z 162 HIS ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 249 HIS d 249 HIS e 163 GLN f 209 GLN h 209 GLN h 219 ASN i 173 ASN j 249 HIS k 162 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.065494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.051819 restraints weight = 203947.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.053233 restraints weight = 136865.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.054245 restraints weight = 103799.803| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 74328 Z= 0.352 Angle : 0.595 9.867 100632 Z= 0.307 Chirality : 0.044 0.287 10944 Planarity : 0.004 0.047 13248 Dihedral : 4.226 22.276 10128 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.24 (0.09), residues: 8976 helix: 1.98 (0.08), residues: 3720 sheet: 0.36 (0.11), residues: 2112 loop : -0.16 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP j 259 HIS 0.005 0.001 HIS a 42 PHE 0.017 0.002 PHE a 175 TYR 0.017 0.001 TYR Z 154 ARG 0.011 0.001 ARG f 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15042.59 seconds wall clock time: 262 minutes 58.22 seconds (15778.22 seconds total)