Starting phenix.real_space_refine on Thu Mar 5 08:13:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.map" model { file = "/net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l7c_0842/03_2026/6l7c_0842.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13005 2.51 5 N 3582 2.21 5 O 3942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20601 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "J" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Restraints were copied for chains: B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, T, U, V, W, X, Y, Z, a Time building chain proxies: 2.02, per 1000 atoms: 0.10 Number of scatterers: 20601 At special positions: 0 Unit cell: (133.32, 134.64, 121.44, 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 72 16.00 O 3942 8.00 N 3582 7.00 C 13005 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: 1.60 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 27 sheets defined 31.2% alpha, 134.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.668A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN B 246 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 247 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 102 removed outlier: 3.551A pdb=" N ASN C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN C 246 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN D 91 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN D 246 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 removed outlier: 3.551A pdb=" N ASN E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 99 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN E 246 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'F' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN F 91 " --> pdb=" O GLN F 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN F 246 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN G 91 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE G 225 " --> pdb=" O GLU G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN G 246 " --> pdb=" O ALA G 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 255 Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 75 removed outlier: 3.668A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE H 225 " --> pdb=" O GLU H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN H 246 " --> pdb=" O ALA H 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 247 " --> pdb=" O GLU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 255 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN I 91 " --> pdb=" O GLN I 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 99 " --> pdb=" O ILE I 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE I 225 " --> pdb=" O GLU I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN I 246 " --> pdb=" O ALA I 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 255 Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 18 through 28 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 28 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 18 through 28 Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 18 through 28 Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 18 through 28 Processing helix chain 'O' and resid 15 through 17 No H-bonds generated for 'chain 'O' and resid 15 through 17' Processing helix chain 'O' and resid 18 through 28 Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 18 through 28 Processing helix chain 'Q' and resid 15 through 17 No H-bonds generated for 'chain 'Q' and resid 15 through 17' Processing helix chain 'Q' and resid 18 through 28 Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 18 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.239A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE B 146 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY B 140 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA B 148 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY B 138 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR B 150 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER B 136 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR B 152 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 134 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 154 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER B 132 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN B 156 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 158 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN A 42 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN I 42 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN G 42 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA G 158 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR G 130 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 156 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER G 132 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 154 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL G 134 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR G 152 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N SER G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR G 150 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY G 138 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA G 148 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY G 140 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE G 146 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 42 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 42 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN E 42 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN F 42 " --> pdb=" O GLY F 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 130 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN F 156 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER F 132 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU F 154 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 134 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR F 152 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR F 150 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY F 138 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA F 148 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N GLY F 140 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE F 146 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 130 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN F 156 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER F 132 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU F 154 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 134 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR F 152 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR F 150 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY F 138 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA F 148 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N GLY F 140 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE F 146 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 136 " --> pdb=" O THR F 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 134 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA G 158 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR G 130 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 156 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER G 132 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 154 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL G 134 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR G 152 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N SER G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR G 150 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY G 138 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA G 148 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY G 140 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE G 146 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE A 34 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU A 81 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 36 " --> pdb=" O LEU A 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE B 34 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 81 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 36 " --> pdb=" O LEU B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE C 34 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU C 81 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 36 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.358A pdb=" N ILE D 34 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D 81 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 36 " --> pdb=" O LEU D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE E 34 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU E 81 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 36 " --> pdb=" O LEU E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE F 34 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU F 81 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 36 " --> pdb=" O LEU F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE G 34 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU G 81 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL G 36 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE H 34 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU H 81 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL H 36 " --> pdb=" O LEU H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.360A pdb=" N ILE I 34 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU I 81 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL I 36 " --> pdb=" O LEU I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 2400 hydrogen bonds defined for protein. 6945 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: 3.96 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6889 1.34 - 1.45: 2714 1.45 - 1.57: 11250 1.57 - 1.68: 0 1.68 - 1.80: 135 Bond restraints: 20988 Sorted by residual: bond pdb=" N ASP D 195 " pdb=" CA ASP D 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.75e+00 bond pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.72e+00 bond pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.43e+00 bond pdb=" N ASP F 195 " pdb=" CA ASP F 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.38e+00 bond pdb=" N ASP I 195 " pdb=" CA ASP I 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.35e+00 ... (remaining 20983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 27776 2.22 - 4.43: 637 4.43 - 6.65: 45 6.65 - 8.87: 9 8.87 - 11.09: 18 Bond angle restraints: 28485 Sorted by residual: angle pdb=" C ILE C 194 " pdb=" N ASP C 195 " pdb=" CA ASP C 195 " ideal model delta sigma weight residual 121.31 132.20 -10.89 1.49e+00 4.50e-01 5.35e+01 angle pdb=" C ILE I 194 " pdb=" N ASP I 195 " pdb=" CA ASP I 195 " ideal model delta sigma weight residual 121.31 132.18 -10.87 1.49e+00 4.50e-01 5.32e+01 angle pdb=" C ILE G 194 " pdb=" N ASP G 195 " pdb=" CA ASP G 195 " ideal model delta sigma weight residual 121.31 132.17 -10.86 1.49e+00 4.50e-01 5.31e+01 angle pdb=" C ILE A 194 " pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 121.31 132.16 -10.85 1.49e+00 4.50e-01 5.30e+01 angle pdb=" C ILE E 194 " pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 121.31 132.16 -10.85 1.49e+00 4.50e-01 5.30e+01 ... (remaining 28480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 10890 15.33 - 30.67: 1332 30.67 - 46.00: 345 46.00 - 61.33: 60 61.33 - 76.67: 36 Dihedral angle restraints: 12663 sinusoidal: 5031 harmonic: 7632 Sorted by residual: dihedral pdb=" CA ASP F 195 " pdb=" C ASP F 195 " pdb=" N TYR F 196 " pdb=" CA TYR F 196 " ideal model delta harmonic sigma weight residual -180.00 -149.64 -30.36 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ASP A 195 " pdb=" C ASP A 195 " pdb=" N TYR A 196 " pdb=" CA TYR A 196 " ideal model delta harmonic sigma weight residual -180.00 -149.69 -30.31 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA ASP E 195 " pdb=" C ASP E 195 " pdb=" N TYR E 196 " pdb=" CA TYR E 196 " ideal model delta harmonic sigma weight residual -180.00 -149.71 -30.29 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 12660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2058 0.038 - 0.076: 761 0.076 - 0.114: 240 0.114 - 0.152: 126 0.152 - 0.190: 19 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CA ILE F 194 " pdb=" N ILE F 194 " pdb=" C ILE F 194 " pdb=" CB ILE F 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ILE I 194 " pdb=" N ILE I 194 " pdb=" C ILE I 194 " pdb=" CB ILE I 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ILE D 194 " pdb=" N ILE D 194 " pdb=" C ILE D 194 " pdb=" CB ILE D 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 3201 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 195 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ASP C 195 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 195 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 195 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ASP H 195 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP H 195 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR H 196 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 195 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ASP E 195 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP E 195 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR E 196 " -0.013 2.00e-02 2.50e+03 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7157 2.86 - 3.37: 17935 3.37 - 3.88: 33553 3.88 - 4.39: 38638 4.39 - 4.90: 68404 Nonbonded interactions: 165687 Sorted by model distance: nonbonded pdb=" O THR E 104 " pdb=" OG SER F 115 " model vdw 2.347 3.040 nonbonded pdb=" O LEU E 72 " pdb=" OG SER E 75 " model vdw 2.366 3.040 nonbonded pdb=" O LEU F 72 " pdb=" OG SER F 75 " model vdw 2.366 3.040 nonbonded pdb=" O LEU A 72 " pdb=" OG SER A 75 " model vdw 2.366 3.040 nonbonded pdb=" O LEU I 72 " pdb=" OG SER I 75 " model vdw 2.366 3.040 ... (remaining 165682 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.006 0.039 20988 Z= 0.254 Angle : 0.855 11.086 28485 Z= 0.498 Chirality : 0.051 0.190 3204 Planarity : 0.006 0.045 3762 Dihedral : 14.849 76.668 7767 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.20 % Allowed : 5.20 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.15), residues: 2601 helix: -4.22 (0.07), residues: 738 sheet: -0.53 (0.19), residues: 765 loop : -1.94 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 93 TYR 0.013 0.002 TYR I 196 PHE 0.019 0.002 PHE F 144 TRP 0.016 0.003 TRP D 237 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00559 (20988) covalent geometry : angle 0.85503 (28485) hydrogen bonds : bond 0.26154 ( 859) hydrogen bonds : angle 9.65370 ( 6945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 507 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8107 (tptm) REVERT: A 42 GLN cc_start: 0.8659 (mp10) cc_final: 0.8381 (mp10) REVERT: A 56 PHE cc_start: 0.9072 (m-10) cc_final: 0.8839 (m-10) REVERT: A 82 GLU cc_start: 0.7657 (tp30) cc_final: 0.7437 (tp30) REVERT: A 124 GLU cc_start: 0.8419 (pt0) cc_final: 0.8121 (pt0) REVERT: A 203 GLU cc_start: 0.7830 (tt0) cc_final: 0.7448 (tt0) REVERT: A 230 ASP cc_start: 0.8509 (t70) cc_final: 0.8092 (t70) REVERT: A 261 GLU cc_start: 0.3168 (OUTLIER) cc_final: 0.2524 (tp30) REVERT: B 22 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8086 (tptm) REVERT: B 44 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 131 GLU cc_start: 0.7676 (tp30) cc_final: 0.7418 (tp30) REVERT: B 135 LYS cc_start: 0.8759 (mttt) cc_final: 0.8494 (mttp) REVERT: B 155 ASP cc_start: 0.8609 (m-30) cc_final: 0.8390 (m-30) REVERT: B 194 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (pt) REVERT: B 230 ASP cc_start: 0.8584 (t70) cc_final: 0.8339 (t70) REVERT: B 261 GLU cc_start: 0.3124 (OUTLIER) cc_final: 0.1902 (tp30) REVERT: C 22 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8101 (tptp) REVERT: C 51 TYR cc_start: 0.8600 (t80) cc_final: 0.8313 (t80) REVERT: C 194 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7898 (pt) REVERT: C 221 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 230 ASP cc_start: 0.8530 (t70) cc_final: 0.8175 (t0) REVERT: C 261 GLU cc_start: 0.3427 (OUTLIER) cc_final: 0.2837 (tp30) REVERT: D 22 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8066 (tptp) REVERT: D 44 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 192 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7555 (ttp80) REVERT: D 194 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (pt) REVERT: D 230 ASP cc_start: 0.8392 (t70) cc_final: 0.7961 (t0) REVERT: D 261 GLU cc_start: 0.3159 (OUTLIER) cc_final: 0.1527 (tp30) REVERT: E 22 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8139 (tptm) REVERT: E 42 GLN cc_start: 0.8515 (mp10) cc_final: 0.8001 (mp10) REVERT: E 44 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 51 TYR cc_start: 0.8518 (t80) cc_final: 0.8238 (t80) REVERT: E 135 LYS cc_start: 0.8751 (mttt) cc_final: 0.8467 (mttm) REVERT: E 194 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7916 (pt) REVERT: E 203 GLU cc_start: 0.7621 (tt0) cc_final: 0.7375 (tt0) REVERT: E 221 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8117 (mt-10) REVERT: E 261 GLU cc_start: 0.3054 (OUTLIER) cc_final: 0.1188 (tp30) REVERT: F 22 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8094 (tptm) REVERT: F 44 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7736 (mt-10) REVERT: F 51 TYR cc_start: 0.8549 (t80) cc_final: 0.8267 (t80) REVERT: F 82 GLU cc_start: 0.7671 (tp30) cc_final: 0.7313 (tp30) REVERT: F 194 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (pt) REVERT: F 230 ASP cc_start: 0.8419 (t70) cc_final: 0.7977 (t0) REVERT: F 261 GLU cc_start: 0.3660 (OUTLIER) cc_final: 0.1349 (tp30) REVERT: G 22 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8110 (tptm) REVERT: G 56 PHE cc_start: 0.9063 (m-10) cc_final: 0.8811 (m-10) REVERT: G 105 VAL cc_start: 0.7367 (t) cc_final: 0.7106 (t) REVERT: G 155 ASP cc_start: 0.8583 (m-30) cc_final: 0.8316 (m-30) REVERT: G 192 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7567 (ttp80) REVERT: G 194 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8100 (pt) REVERT: G 221 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 261 GLU cc_start: 0.3244 (OUTLIER) cc_final: 0.1569 (tp30) REVERT: H 22 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8272 (tptm) REVERT: H 131 GLU cc_start: 0.7763 (tp30) cc_final: 0.7455 (tp30) REVERT: H 194 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8298 (pt) REVERT: H 261 GLU cc_start: 0.2946 (OUTLIER) cc_final: 0.2522 (tp30) REVERT: I 22 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8225 (tptm) REVERT: I 44 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7839 (mt-10) REVERT: I 230 ASP cc_start: 0.8515 (t70) cc_final: 0.8008 (t0) REVERT: I 261 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.1712 (tp30) REVERT: J 4 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8566 (p) REVERT: K 6 GLN cc_start: 0.8100 (mt0) cc_final: 0.7852 (mm-40) REVERT: M 17 ASN cc_start: 0.9079 (m110) cc_final: 0.8858 (m-40) outliers start: 27 outliers final: 5 residues processed: 519 average time/residue: 0.1727 time to fit residues: 131.3488 Evaluate side-chains 374 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN D 100 GLN E 100 GLN F 100 GLN G 100 GLN H 100 GLN I 100 GLN K 17 ASN L 29 GLN M 17 ASN M 29 GLN N 29 GLN O 17 ASN O 29 GLN P 29 GLN Q 17 ASN R 17 ASN a 5 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096458 restraints weight = 32473.124| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.28 r_work: 0.2949 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20988 Z= 0.203 Angle : 0.648 8.338 28485 Z= 0.345 Chirality : 0.046 0.178 3204 Planarity : 0.005 0.039 3762 Dihedral : 5.791 39.312 2918 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.69 % Allowed : 12.22 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2601 helix: -1.43 (0.15), residues: 765 sheet: 0.08 (0.19), residues: 756 loop : -1.35 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 8 TYR 0.011 0.001 TYR A 184 PHE 0.028 0.002 PHE E 144 TRP 0.011 0.001 TRP H 237 HIS 0.002 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00474 (20988) covalent geometry : angle 0.64766 (28485) hydrogen bonds : bond 0.04796 ( 859) hydrogen bonds : angle 3.54579 ( 6945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 373 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8332 (tptm) REVERT: A 44 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 203 GLU cc_start: 0.8469 (tt0) cc_final: 0.8144 (tt0) REVERT: A 246 GLN cc_start: 0.8031 (pp30) cc_final: 0.7831 (pp30) REVERT: B 22 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8258 (tptm) REVERT: B 44 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8439 (mt-10) REVERT: B 135 LYS cc_start: 0.8940 (mttt) cc_final: 0.8721 (mttp) REVERT: C 22 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8200 (tptp) REVERT: C 51 TYR cc_start: 0.8807 (t80) cc_final: 0.8581 (t80) REVERT: C 100 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: C 230 ASP cc_start: 0.8635 (t70) cc_final: 0.8426 (t70) REVERT: C 245 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7825 (ttm110) REVERT: D 22 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8294 (tptp) REVERT: D 212 VAL cc_start: 0.9028 (p) cc_final: 0.8799 (t) REVERT: E 22 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8397 (tptm) REVERT: E 44 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8362 (mt-10) REVERT: E 51 TYR cc_start: 0.8731 (t80) cc_final: 0.8425 (t80) REVERT: E 201 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6377 (tm-30) REVERT: F 22 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8266 (tptm) REVERT: F 230 ASP cc_start: 0.8713 (t70) cc_final: 0.8367 (t70) REVERT: G 22 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8443 (tmtt) REVERT: H 22 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8451 (tptm) REVERT: H 238 ASP cc_start: 0.8031 (t0) cc_final: 0.7782 (t0) REVERT: I 22 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8399 (tptm) REVERT: I 43 ASP cc_start: 0.8361 (t70) cc_final: 0.8102 (t70) REVERT: I 44 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8239 (mt-10) REVERT: I 56 PHE cc_start: 0.9369 (m-80) cc_final: 0.9047 (m-80) REVERT: I 122 MET cc_start: 0.8413 (ptp) cc_final: 0.8115 (ptm) REVERT: J 4 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (p) REVERT: J 33 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7904 (mmtm) REVERT: K 6 GLN cc_start: 0.8310 (mt0) cc_final: 0.8070 (mm-40) REVERT: Q 27 GLN cc_start: 0.9105 (mt0) cc_final: 0.8857 (mm-40) outliers start: 38 outliers final: 16 residues processed: 398 average time/residue: 0.1601 time to fit residues: 96.9309 Evaluate side-chains 360 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 342 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 144 PHE Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN K 29 GLN M 29 GLN Q 29 GLN R 29 GLN S 5 GLN ** U 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 GLN X 5 GLN Y 5 GLN ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 5 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096737 restraints weight = 32509.899| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.29 r_work: 0.2960 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20988 Z= 0.151 Angle : 0.588 7.855 28485 Z= 0.314 Chirality : 0.045 0.166 3204 Planarity : 0.004 0.038 3762 Dihedral : 4.862 26.629 2874 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.87 % Allowed : 15.42 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2601 helix: 0.34 (0.18), residues: 765 sheet: 0.39 (0.19), residues: 747 loop : -1.09 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 8 TYR 0.017 0.001 TYR A 184 PHE 0.025 0.002 PHE H 144 TRP 0.005 0.001 TRP D 237 HIS 0.001 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00348 (20988) covalent geometry : angle 0.58804 (28485) hydrogen bonds : bond 0.03911 ( 859) hydrogen bonds : angle 3.06914 ( 6945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8266 (tptm) REVERT: A 44 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 203 GLU cc_start: 0.8443 (tt0) cc_final: 0.8031 (tt0) REVERT: A 246 GLN cc_start: 0.8123 (pp30) cc_final: 0.7897 (pp30) REVERT: B 22 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8234 (tptm) REVERT: B 82 GLU cc_start: 0.8129 (tp30) cc_final: 0.7661 (tp30) REVERT: C 22 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8246 (tptp) REVERT: C 245 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7900 (ttm110) REVERT: D 22 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8302 (tptp) REVERT: D 213 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8170 (ptm) REVERT: E 22 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8371 (tptm) REVERT: E 44 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8337 (mt-10) REVERT: E 51 TYR cc_start: 0.8621 (t80) cc_final: 0.8278 (t80) REVERT: E 201 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6363 (tm-30) REVERT: F 22 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8285 (tptm) REVERT: F 230 ASP cc_start: 0.8741 (t70) cc_final: 0.8437 (t70) REVERT: G 22 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8393 (tmtt) REVERT: G 155 ASP cc_start: 0.8736 (m-30) cc_final: 0.8484 (m-30) REVERT: H 22 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8417 (tptm) REVERT: H 44 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7996 (mt-10) REVERT: H 113 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8650 (pp) REVERT: H 217 MET cc_start: 0.8530 (tpp) cc_final: 0.7963 (tpp) REVERT: H 238 ASP cc_start: 0.8068 (t0) cc_final: 0.7775 (t0) REVERT: I 22 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8303 (tptm) REVERT: I 43 ASP cc_start: 0.8234 (t70) cc_final: 0.7990 (t70) REVERT: I 44 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8181 (mt-10) REVERT: I 201 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6356 (tm-30) REVERT: I 213 MET cc_start: 0.8986 (ptp) cc_final: 0.8605 (ptt) REVERT: I 238 ASP cc_start: 0.8326 (m-30) cc_final: 0.8108 (t0) REVERT: K 6 GLN cc_start: 0.8343 (mt0) cc_final: 0.8102 (mm-40) REVERT: R 27 GLN cc_start: 0.8959 (mt0) cc_final: 0.8602 (mm110) REVERT: V 5 GLN cc_start: 0.7206 (mt0) cc_final: 0.6920 (mt0) outliers start: 42 outliers final: 18 residues processed: 385 average time/residue: 0.1465 time to fit residues: 87.4326 Evaluate side-chains 352 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 332 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 5 GLN Y 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097473 restraints weight = 32372.260| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.25 r_work: 0.2949 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20988 Z= 0.171 Angle : 0.605 7.894 28485 Z= 0.319 Chirality : 0.046 0.169 3204 Planarity : 0.004 0.064 3762 Dihedral : 4.749 24.427 2871 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 16.62 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2601 helix: 1.16 (0.19), residues: 765 sheet: 0.55 (0.19), residues: 747 loop : -0.86 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 8 TYR 0.018 0.001 TYR H 184 PHE 0.029 0.002 PHE A 144 TRP 0.006 0.001 TRP A 237 HIS 0.002 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00403 (20988) covalent geometry : angle 0.60514 (28485) hydrogen bonds : bond 0.03739 ( 859) hydrogen bonds : angle 2.97390 ( 6945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8239 (tptm) REVERT: A 196 TYR cc_start: 0.8420 (t80) cc_final: 0.8086 (t80) REVERT: A 246 GLN cc_start: 0.8133 (pp30) cc_final: 0.7855 (pp30) REVERT: B 22 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8295 (tptm) REVERT: B 82 GLU cc_start: 0.8429 (tp30) cc_final: 0.7995 (tp30) REVERT: B 113 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8888 (pp) REVERT: C 22 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8279 (tptp) REVERT: C 82 GLU cc_start: 0.8270 (tp30) cc_final: 0.8043 (tp30) REVERT: D 22 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8367 (tptp) REVERT: D 51 TYR cc_start: 0.9017 (t80) cc_final: 0.8697 (t80) REVERT: D 113 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8548 (pp) REVERT: D 213 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8196 (ptm) REVERT: D 245 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8139 (ttm170) REVERT: E 22 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8375 (tptm) REVERT: E 44 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 51 TYR cc_start: 0.8726 (t80) cc_final: 0.8423 (t80) REVERT: E 201 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6914 (tm-30) REVERT: E 203 GLU cc_start: 0.8670 (tt0) cc_final: 0.8396 (tt0) REVERT: E 221 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8740 (mt-10) REVERT: F 22 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8324 (tptm) REVERT: F 201 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6711 (tm-30) REVERT: F 230 ASP cc_start: 0.8863 (t70) cc_final: 0.8607 (t70) REVERT: G 22 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8390 (tmtt) REVERT: G 113 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8688 (pp) REVERT: G 166 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.8994 (p) REVERT: H 22 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8405 (tptm) REVERT: H 213 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8368 (ptm) REVERT: H 238 ASP cc_start: 0.8400 (t0) cc_final: 0.8116 (t0) REVERT: I 22 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8311 (tptm) REVERT: I 43 ASP cc_start: 0.8368 (t70) cc_final: 0.8160 (t70) REVERT: I 44 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8364 (mt-10) REVERT: I 82 GLU cc_start: 0.8311 (tp30) cc_final: 0.7868 (tp30) REVERT: I 201 GLU cc_start: 0.7635 (tm-30) cc_final: 0.6611 (tm-30) REVERT: I 213 MET cc_start: 0.9040 (ptp) cc_final: 0.8691 (ptt) REVERT: I 238 ASP cc_start: 0.8578 (m-30) cc_final: 0.8226 (t0) REVERT: J 33 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7895 (mmtm) REVERT: K 6 GLN cc_start: 0.8478 (mt0) cc_final: 0.8185 (mm-40) REVERT: R 27 GLN cc_start: 0.8985 (mt0) cc_final: 0.8662 (mm-40) REVERT: X 5 GLN cc_start: 0.7536 (mt0) cc_final: 0.7115 (mt0) outliers start: 55 outliers final: 29 residues processed: 386 average time/residue: 0.1531 time to fit residues: 90.6112 Evaluate side-chains 375 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain R residue 4 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 24 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN G 100 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN M 29 GLN V 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097777 restraints weight = 32319.853| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.24 r_work: 0.2960 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20988 Z= 0.157 Angle : 0.585 7.523 28485 Z= 0.308 Chirality : 0.045 0.163 3204 Planarity : 0.003 0.035 3762 Dihedral : 4.665 26.007 2871 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.02 % Allowed : 16.18 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2601 helix: 1.55 (0.20), residues: 765 sheet: 0.66 (0.19), residues: 747 loop : -0.66 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 8 TYR 0.018 0.001 TYR H 184 PHE 0.025 0.002 PHE A 144 TRP 0.005 0.001 TRP A 237 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00368 (20988) covalent geometry : angle 0.58516 (28485) hydrogen bonds : bond 0.03584 ( 859) hydrogen bonds : angle 2.86725 ( 6945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8233 (tptm) REVERT: A 44 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8253 (mt-10) REVERT: A 196 TYR cc_start: 0.8489 (t80) cc_final: 0.8199 (t80) REVERT: A 246 GLN cc_start: 0.8181 (pp30) cc_final: 0.7912 (pp30) REVERT: B 22 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8314 (tptm) REVERT: B 82 GLU cc_start: 0.8466 (tp30) cc_final: 0.8062 (tp30) REVERT: B 113 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8843 (pp) REVERT: B 117 THR cc_start: 0.9361 (m) cc_final: 0.9141 (t) REVERT: C 22 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8340 (tptp) REVERT: C 245 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8004 (ttm110) REVERT: D 22 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8370 (tptp) REVERT: D 51 TYR cc_start: 0.9022 (t80) cc_final: 0.8703 (t80) REVERT: D 201 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: D 213 MET cc_start: 0.8601 (ptp) cc_final: 0.8187 (ptt) REVERT: E 22 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8326 (tptm) REVERT: E 44 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8614 (mt-10) REVERT: E 51 TYR cc_start: 0.8716 (t80) cc_final: 0.8431 (t80) REVERT: E 192 ARG cc_start: 0.8452 (ttp80) cc_final: 0.7928 (ttp80) REVERT: E 201 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6872 (tm-30) REVERT: E 221 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8706 (mt-10) REVERT: F 22 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8319 (tptm) REVERT: F 201 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6649 (tm-30) REVERT: F 230 ASP cc_start: 0.8879 (t70) cc_final: 0.8623 (t70) REVERT: G 22 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8373 (tmtt) REVERT: G 100 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7747 (mm-40) REVERT: G 113 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8708 (pp) REVERT: G 166 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.8996 (p) REVERT: G 234 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7423 (mtm110) REVERT: H 22 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8414 (tptm) REVERT: H 213 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8382 (ptm) REVERT: H 238 ASP cc_start: 0.8309 (t0) cc_final: 0.8020 (t0) REVERT: I 22 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8290 (tptm) REVERT: I 43 ASP cc_start: 0.8359 (t70) cc_final: 0.8145 (t70) REVERT: I 44 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8369 (mt-10) REVERT: I 82 GLU cc_start: 0.8384 (tp30) cc_final: 0.7929 (tp30) REVERT: I 166 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8935 (p) REVERT: I 201 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6581 (tm-30) REVERT: I 213 MET cc_start: 0.9023 (ptp) cc_final: 0.8685 (ptt) REVERT: I 238 ASP cc_start: 0.8551 (m-30) cc_final: 0.8220 (t0) REVERT: J 33 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7896 (mmtm) REVERT: K 6 GLN cc_start: 0.8374 (mt0) cc_final: 0.8127 (mm-40) REVERT: Q 11 ASN cc_start: 0.9154 (m-40) cc_final: 0.8912 (m-40) REVERT: R 27 GLN cc_start: 0.8934 (mt0) cc_final: 0.8653 (mm-40) outliers start: 68 outliers final: 42 residues processed: 403 average time/residue: 0.1510 time to fit residues: 94.3691 Evaluate side-chains 391 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain R residue 4 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 231 optimal weight: 0.0870 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN O 29 GLN Q 27 GLN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN a 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098921 restraints weight = 32104.846| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.24 r_work: 0.2966 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20988 Z= 0.134 Angle : 0.565 7.287 28485 Z= 0.299 Chirality : 0.045 0.160 3204 Planarity : 0.003 0.025 3762 Dihedral : 4.545 25.150 2871 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.07 % Allowed : 15.96 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2601 helix: 1.78 (0.20), residues: 765 sheet: 0.80 (0.19), residues: 747 loop : -0.51 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 8 TYR 0.016 0.001 TYR H 184 PHE 0.023 0.001 PHE A 144 TRP 0.003 0.001 TRP C 77 HIS 0.002 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00312 (20988) covalent geometry : angle 0.56546 (28485) hydrogen bonds : bond 0.03415 ( 859) hydrogen bonds : angle 2.75192 ( 6945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 353 time to evaluate : 0.820 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: A 22 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8209 (tptm) REVERT: A 44 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 196 TYR cc_start: 0.8449 (t80) cc_final: 0.8220 (t80) REVERT: A 246 GLN cc_start: 0.8142 (pp30) cc_final: 0.7934 (pp30) REVERT: B 22 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8271 (tptm) REVERT: B 82 GLU cc_start: 0.8477 (tp30) cc_final: 0.8065 (tp30) REVERT: B 113 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 117 THR cc_start: 0.9355 (m) cc_final: 0.9139 (t) REVERT: B 203 GLU cc_start: 0.8610 (tt0) cc_final: 0.8334 (tt0) REVERT: C 22 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8317 (tptp) REVERT: C 245 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7913 (ttm110) REVERT: D 22 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8357 (tptp) REVERT: D 51 TYR cc_start: 0.8959 (t80) cc_final: 0.8604 (t80) REVERT: D 201 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: D 203 GLU cc_start: 0.8667 (tt0) cc_final: 0.8416 (tt0) REVERT: D 213 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8143 (ptt) REVERT: E 22 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8298 (tptm) REVERT: E 44 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 51 TYR cc_start: 0.8688 (t80) cc_final: 0.8402 (t80) REVERT: E 201 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6844 (tm-30) REVERT: E 203 GLU cc_start: 0.8742 (tt0) cc_final: 0.8506 (tt0) REVERT: E 256 MET cc_start: 0.8452 (ttm) cc_final: 0.8182 (ttm) REVERT: F 22 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8260 (tptm) REVERT: F 201 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6630 (tm-30) REVERT: F 203 GLU cc_start: 0.8543 (tt0) cc_final: 0.8310 (tt0) REVERT: F 230 ASP cc_start: 0.8860 (t70) cc_final: 0.8605 (t70) REVERT: G 22 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8358 (tmtt) REVERT: G 113 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8666 (pp) REVERT: G 166 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8977 (p) REVERT: G 234 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7339 (mtm110) REVERT: H 22 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8389 (tptm) REVERT: H 44 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8252 (mt-10) REVERT: H 213 MET cc_start: 0.8703 (ptp) cc_final: 0.8373 (ptm) REVERT: H 238 ASP cc_start: 0.8315 (t0) cc_final: 0.8029 (t0) REVERT: I 22 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8278 (tptm) REVERT: I 43 ASP cc_start: 0.8325 (t70) cc_final: 0.8111 (t70) REVERT: I 44 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8337 (mt-10) REVERT: I 82 GLU cc_start: 0.8385 (tp30) cc_final: 0.7913 (tp30) REVERT: I 166 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8929 (p) REVERT: I 201 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6657 (tm-30) REVERT: I 213 MET cc_start: 0.9023 (ptp) cc_final: 0.8676 (ptt) REVERT: I 238 ASP cc_start: 0.8559 (m-30) cc_final: 0.8239 (t0) REVERT: J 27 GLN cc_start: 0.9334 (mm-40) cc_final: 0.9126 (mm110) REVERT: J 33 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7932 (mmtm) REVERT: K 6 GLN cc_start: 0.8368 (mt0) cc_final: 0.8099 (mm-40) REVERT: K 32 TYR cc_start: 0.8400 (m-80) cc_final: 0.8003 (m-80) REVERT: Q 11 ASN cc_start: 0.9121 (m-40) cc_final: 0.8890 (m-40) REVERT: R 27 GLN cc_start: 0.8927 (mt0) cc_final: 0.8658 (mm-40) outliers start: 69 outliers final: 48 residues processed: 400 average time/residue: 0.1450 time to fit residues: 89.8491 Evaluate side-chains 395 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain R residue 4 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 1 optimal weight: 0.0370 chunk 137 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN J 11 ASN L 11 ASN M 27 GLN O 29 GLN W 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099280 restraints weight = 32183.827| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.25 r_work: 0.2980 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20988 Z= 0.133 Angle : 0.573 12.107 28485 Z= 0.303 Chirality : 0.045 0.158 3204 Planarity : 0.003 0.028 3762 Dihedral : 4.510 26.310 2871 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.98 % Allowed : 16.84 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2601 helix: 1.94 (0.20), residues: 765 sheet: 0.87 (0.19), residues: 747 loop : -0.37 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 8 TYR 0.015 0.001 TYR H 184 PHE 0.024 0.001 PHE R 5 TRP 0.003 0.001 TRP H 77 HIS 0.001 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00310 (20988) covalent geometry : angle 0.57350 (28485) hydrogen bonds : bond 0.03360 ( 859) hydrogen bonds : angle 2.70705 ( 6945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 350 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8267 (tptm) REVERT: A 44 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 203 GLU cc_start: 0.8645 (tt0) cc_final: 0.8421 (tt0) REVERT: A 246 GLN cc_start: 0.8151 (pp30) cc_final: 0.7935 (pp30) REVERT: B 22 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8288 (tptm) REVERT: B 82 GLU cc_start: 0.8472 (tp30) cc_final: 0.8240 (tp30) REVERT: B 113 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8823 (pp) REVERT: B 117 THR cc_start: 0.9355 (m) cc_final: 0.9150 (t) REVERT: B 192 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7864 (ttt90) REVERT: B 203 GLU cc_start: 0.8668 (tt0) cc_final: 0.8372 (tt0) REVERT: B 241 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8754 (t0) REVERT: C 22 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8315 (tptp) REVERT: C 245 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7848 (ttm110) REVERT: D 22 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8357 (tptp) REVERT: D 51 TYR cc_start: 0.8977 (t80) cc_final: 0.8635 (t80) REVERT: D 201 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: D 213 MET cc_start: 0.8630 (ptp) cc_final: 0.8140 (ptt) REVERT: D 245 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7795 (ttm110) REVERT: E 22 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8300 (tptm) REVERT: E 44 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8615 (mt-10) REVERT: E 51 TYR cc_start: 0.8743 (t80) cc_final: 0.8492 (t80) REVERT: E 192 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8139 (ttt180) REVERT: E 201 GLU cc_start: 0.7557 (tm-30) cc_final: 0.6818 (tm-30) REVERT: F 22 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8183 (tptm) REVERT: F 201 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6522 (tm-30) REVERT: F 203 GLU cc_start: 0.8549 (tt0) cc_final: 0.8303 (tt0) REVERT: F 230 ASP cc_start: 0.8875 (t70) cc_final: 0.8621 (t70) REVERT: F 241 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8493 (t0) REVERT: G 22 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8356 (tmtt) REVERT: G 113 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8605 (pp) REVERT: G 166 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9039 (p) REVERT: G 234 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7323 (mtm110) REVERT: G 238 ASP cc_start: 0.8818 (m-30) cc_final: 0.8458 (t0) REVERT: H 22 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8399 (tptm) REVERT: H 214 LEU cc_start: 0.8382 (tp) cc_final: 0.8167 (mp) REVERT: H 238 ASP cc_start: 0.8359 (t0) cc_final: 0.8081 (t0) REVERT: I 22 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8252 (tptm) REVERT: I 44 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8338 (mt-10) REVERT: I 82 GLU cc_start: 0.8385 (tp30) cc_final: 0.7901 (tp30) REVERT: I 166 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (p) REVERT: I 192 ARG cc_start: 0.8397 (ttp80) cc_final: 0.7956 (ttp80) REVERT: I 201 GLU cc_start: 0.7627 (tm-30) cc_final: 0.6670 (tm-30) REVERT: I 213 MET cc_start: 0.8989 (ptp) cc_final: 0.8752 (ptt) REVERT: I 238 ASP cc_start: 0.8533 (m-30) cc_final: 0.8227 (t0) REVERT: J 33 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7936 (mmtm) REVERT: K 6 GLN cc_start: 0.8341 (mt0) cc_final: 0.8070 (mm-40) REVERT: K 32 TYR cc_start: 0.8447 (m-80) cc_final: 0.8070 (m-80) REVERT: Q 11 ASN cc_start: 0.9090 (m-40) cc_final: 0.8865 (m-40) REVERT: R 27 GLN cc_start: 0.8928 (mt0) cc_final: 0.8674 (mm-40) REVERT: R 32 TYR cc_start: 0.8633 (m-80) cc_final: 0.8419 (m-80) outliers start: 67 outliers final: 44 residues processed: 395 average time/residue: 0.1465 time to fit residues: 89.8778 Evaluate side-chains 390 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 217 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN J 11 ASN J 27 GLN K 27 GLN L 11 ASN O 29 GLN P 29 GLN W 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100179 restraints weight = 32278.860| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.25 r_work: 0.2993 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20988 Z= 0.123 Angle : 0.569 11.788 28485 Z= 0.300 Chirality : 0.044 0.157 3204 Planarity : 0.003 0.028 3762 Dihedral : 4.424 25.460 2871 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.53 % Allowed : 17.47 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2601 helix: 2.11 (0.20), residues: 765 sheet: 0.93 (0.19), residues: 747 loop : -0.30 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 8 TYR 0.015 0.001 TYR H 184 PHE 0.021 0.001 PHE R 5 TRP 0.003 0.001 TRP H 77 HIS 0.001 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00285 (20988) covalent geometry : angle 0.56888 (28485) hydrogen bonds : bond 0.03271 ( 859) hydrogen bonds : angle 2.64546 ( 6945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 360 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8258 (tptm) REVERT: A 44 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 22 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8270 (tptm) REVERT: B 82 GLU cc_start: 0.8464 (tp30) cc_final: 0.8050 (tp30) REVERT: B 113 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 203 GLU cc_start: 0.8648 (tt0) cc_final: 0.8359 (tt0) REVERT: C 22 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8294 (tptp) REVERT: C 245 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7713 (ttm110) REVERT: D 22 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8340 (tptp) REVERT: D 51 TYR cc_start: 0.8966 (t80) cc_final: 0.8622 (t80) REVERT: D 201 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: D 203 GLU cc_start: 0.8662 (tt0) cc_final: 0.8389 (tt0) REVERT: D 213 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8071 (ptt) REVERT: D 245 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7780 (ttm110) REVERT: E 22 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8240 (tptm) REVERT: E 44 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8475 (mt-10) REVERT: E 51 TYR cc_start: 0.8739 (t80) cc_final: 0.8496 (t80) REVERT: E 192 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8091 (ttt180) REVERT: E 201 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6809 (tm-30) REVERT: E 203 GLU cc_start: 0.8748 (tt0) cc_final: 0.8470 (tt0) REVERT: F 22 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8183 (tptm) REVERT: F 166 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8786 (p) REVERT: F 192 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8055 (ttp80) REVERT: F 201 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6555 (tm-30) REVERT: F 203 GLU cc_start: 0.8518 (tt0) cc_final: 0.8298 (tt0) REVERT: F 230 ASP cc_start: 0.8854 (t70) cc_final: 0.8598 (t70) REVERT: F 241 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8484 (t0) REVERT: G 22 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8324 (tmtt) REVERT: G 113 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8596 (pp) REVERT: G 166 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9015 (p) REVERT: G 234 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7240 (mtm110) REVERT: G 238 ASP cc_start: 0.8830 (m-30) cc_final: 0.8470 (t0) REVERT: H 22 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8393 (tptm) REVERT: H 238 ASP cc_start: 0.8352 (t0) cc_final: 0.8080 (t0) REVERT: I 22 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8223 (tptm) REVERT: I 42 GLN cc_start: 0.8525 (mp10) cc_final: 0.8277 (mt0) REVERT: I 44 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8169 (mt-10) REVERT: I 82 GLU cc_start: 0.8391 (tp30) cc_final: 0.7836 (tp30) REVERT: I 166 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8896 (p) REVERT: I 192 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7957 (ttp80) REVERT: I 201 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6664 (tm-30) REVERT: I 213 MET cc_start: 0.8965 (ptp) cc_final: 0.8724 (ptt) REVERT: I 234 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7518 (mtm110) REVERT: I 238 ASP cc_start: 0.8518 (m-30) cc_final: 0.8228 (t0) REVERT: K 6 GLN cc_start: 0.8345 (mt0) cc_final: 0.8076 (mm-40) REVERT: K 32 TYR cc_start: 0.8421 (m-80) cc_final: 0.8107 (m-80) REVERT: Q 11 ASN cc_start: 0.9071 (m-40) cc_final: 0.8852 (m-40) REVERT: R 27 GLN cc_start: 0.8923 (mt0) cc_final: 0.8663 (mm-40) outliers start: 57 outliers final: 37 residues processed: 401 average time/residue: 0.1434 time to fit residues: 89.1168 Evaluate side-chains 396 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN O 29 GLN ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095652 restraints weight = 32305.332| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.23 r_work: 0.2930 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20988 Z= 0.206 Angle : 0.647 12.772 28485 Z= 0.340 Chirality : 0.046 0.168 3204 Planarity : 0.004 0.028 3762 Dihedral : 4.710 24.596 2871 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.44 % Allowed : 18.04 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2601 helix: 2.02 (0.20), residues: 765 sheet: 0.83 (0.19), residues: 756 loop : -0.33 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 142 TYR 0.016 0.001 TYR E 206 PHE 0.025 0.002 PHE A 144 TRP 0.006 0.001 TRP H 237 HIS 0.002 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00490 (20988) covalent geometry : angle 0.64654 (28485) hydrogen bonds : bond 0.03764 ( 859) hydrogen bonds : angle 2.93619 ( 6945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8235 (tptm) REVERT: B 22 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8208 (tptm) REVERT: B 82 GLU cc_start: 0.8441 (tp30) cc_final: 0.8084 (tp30) REVERT: B 84 GLN cc_start: 0.8526 (tt0) cc_final: 0.8287 (tt0) REVERT: B 113 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 135 LYS cc_start: 0.9055 (mttt) cc_final: 0.8778 (mttp) REVERT: C 22 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8319 (tptp) REVERT: C 82 GLU cc_start: 0.8398 (tp30) cc_final: 0.8103 (tp30) REVERT: C 214 LEU cc_start: 0.8326 (tp) cc_final: 0.7979 (mt) REVERT: C 245 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7825 (ttm110) REVERT: D 22 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8332 (tptp) REVERT: D 51 TYR cc_start: 0.8985 (t80) cc_final: 0.8707 (t80) REVERT: D 201 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: D 213 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8172 (ptt) REVERT: E 22 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8317 (tptm) REVERT: E 44 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8541 (mt-10) REVERT: E 51 TYR cc_start: 0.8729 (t80) cc_final: 0.8472 (t80) REVERT: E 196 TYR cc_start: 0.8339 (t80) cc_final: 0.8003 (t80) REVERT: E 201 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7021 (tm-30) REVERT: E 203 GLU cc_start: 0.8740 (tt0) cc_final: 0.8498 (tt0) REVERT: F 22 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8272 (tptm) REVERT: F 201 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6540 (tm-30) REVERT: F 203 GLU cc_start: 0.8579 (tt0) cc_final: 0.8316 (tt0) REVERT: F 230 ASP cc_start: 0.8901 (t70) cc_final: 0.8661 (t70) REVERT: G 22 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8336 (tmtt) REVERT: G 113 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8681 (pp) REVERT: G 166 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.8985 (p) REVERT: G 203 GLU cc_start: 0.8735 (tt0) cc_final: 0.8461 (tt0) REVERT: G 234 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7277 (mtm110) REVERT: H 22 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8388 (tptm) REVERT: H 238 ASP cc_start: 0.8315 (t0) cc_final: 0.7986 (t0) REVERT: I 22 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8242 (tptm) REVERT: I 44 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8351 (mt-10) REVERT: I 166 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8944 (p) REVERT: I 201 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6560 (tm-30) REVERT: I 234 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7827 (mtm110) REVERT: J 33 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7964 (mmtm) REVERT: K 6 GLN cc_start: 0.8350 (mt0) cc_final: 0.8136 (mt0) REVERT: K 32 TYR cc_start: 0.8426 (m-80) cc_final: 0.8050 (m-80) REVERT: N 11 ASN cc_start: 0.8893 (m-40) cc_final: 0.8583 (m-40) REVERT: R 27 GLN cc_start: 0.8893 (mt0) cc_final: 0.8637 (mm-40) outliers start: 55 outliers final: 42 residues processed: 386 average time/residue: 0.1521 time to fit residues: 90.2350 Evaluate side-chains 372 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 228 optimal weight: 0.1980 chunk 171 optimal weight: 0.6980 chunk 126 optimal weight: 0.0170 chunk 232 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN F 100 GLN J 11 ASN L 11 ASN O 29 GLN ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100814 restraints weight = 32078.679| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.26 r_work: 0.3004 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20988 Z= 0.117 Angle : 0.578 11.333 28485 Z= 0.307 Chirality : 0.044 0.159 3204 Planarity : 0.003 0.029 3762 Dihedral : 4.461 26.559 2871 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 18.53 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2601 helix: 2.10 (0.20), residues: 783 sheet: 0.87 (0.20), residues: 756 loop : -0.42 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 8 TYR 0.016 0.001 TYR E 184 PHE 0.021 0.001 PHE L 12 TRP 0.004 0.001 TRP F 77 HIS 0.001 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00268 (20988) covalent geometry : angle 0.57823 (28485) hydrogen bonds : bond 0.03219 ( 859) hydrogen bonds : angle 2.59251 ( 6945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8237 (tptm) REVERT: A 44 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7964 (mt-10) REVERT: B 22 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8136 (tptm) REVERT: B 82 GLU cc_start: 0.8173 (tp30) cc_final: 0.7923 (tp30) REVERT: B 113 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 192 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7817 (ttt90) REVERT: B 203 GLU cc_start: 0.8343 (tt0) cc_final: 0.8042 (tt0) REVERT: C 22 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8232 (tptp) REVERT: C 214 LEU cc_start: 0.8108 (tp) cc_final: 0.7854 (mt) REVERT: C 245 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7637 (ttm110) REVERT: D 22 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8283 (tptp) REVERT: D 51 TYR cc_start: 0.8852 (t80) cc_final: 0.8499 (t80) REVERT: D 201 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: D 213 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7853 (ptt) REVERT: E 22 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8300 (tptm) REVERT: E 51 TYR cc_start: 0.8589 (t80) cc_final: 0.8336 (t80) REVERT: E 82 GLU cc_start: 0.8225 (tp30) cc_final: 0.7987 (tp30) REVERT: E 192 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7897 (ttt180) REVERT: E 201 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6395 (tm-30) REVERT: E 203 GLU cc_start: 0.8461 (tt0) cc_final: 0.8236 (tt0) REVERT: F 22 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8146 (tptm) REVERT: F 192 ARG cc_start: 0.8576 (ttp80) cc_final: 0.7999 (ttp80) REVERT: F 201 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6307 (tm-30) REVERT: F 230 ASP cc_start: 0.8719 (t70) cc_final: 0.8474 (t70) REVERT: G 113 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8624 (pp) REVERT: G 166 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8965 (p) REVERT: G 238 ASP cc_start: 0.8505 (m-30) cc_final: 0.8263 (t0) REVERT: H 22 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8351 (tptm) REVERT: H 238 ASP cc_start: 0.8000 (t0) cc_final: 0.7686 (t0) REVERT: I 22 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8143 (tptm) REVERT: I 44 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8015 (mt-10) REVERT: I 166 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8858 (p) REVERT: I 192 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7767 (ttp80) REVERT: I 201 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6364 (tm-30) REVERT: I 234 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7395 (mtm110) REVERT: I 238 ASP cc_start: 0.8290 (m-30) cc_final: 0.8047 (t0) REVERT: K 6 GLN cc_start: 0.8197 (mt0) cc_final: 0.7939 (mm-40) REVERT: K 32 TYR cc_start: 0.8496 (m-80) cc_final: 0.8176 (m-80) REVERT: L 25 SER cc_start: 0.9227 (p) cc_final: 0.9021 (p) REVERT: N 11 ASN cc_start: 0.8548 (m-40) cc_final: 0.8341 (m-40) REVERT: R 27 GLN cc_start: 0.8843 (mt0) cc_final: 0.8400 (mm110) outliers start: 46 outliers final: 34 residues processed: 377 average time/residue: 0.1454 time to fit residues: 85.2487 Evaluate side-chains 372 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 156 optimal weight: 0.0870 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 226 optimal weight: 0.0170 chunk 180 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN F 100 GLN J 11 ASN K 27 GLN L 11 ASN ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099817 restraints weight = 32340.426| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.28 r_work: 0.2985 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20988 Z= 0.121 Angle : 0.584 11.953 28485 Z= 0.307 Chirality : 0.044 0.155 3204 Planarity : 0.003 0.029 3762 Dihedral : 4.399 25.782 2871 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 18.62 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2601 helix: 2.29 (0.20), residues: 765 sheet: 0.90 (0.20), residues: 756 loop : -0.22 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 245 TYR 0.017 0.001 TYR E 184 PHE 0.019 0.001 PHE R 5 TRP 0.003 0.001 TRP I 77 HIS 0.001 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00280 (20988) covalent geometry : angle 0.58383 (28485) hydrogen bonds : bond 0.03235 ( 859) hydrogen bonds : angle 2.59168 ( 6945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4176.90 seconds wall clock time: 72 minutes 34.70 seconds (4354.70 seconds total)