Starting phenix.real_space_refine on Thu Sep 26 15:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3x_30073/09_2024/6m3x_30073.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 480 5.16 5 C 38904 2.51 5 N 10080 2.21 5 O 12899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62387 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2505 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 289} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "E" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "G" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "I" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "L" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "O" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "P" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "Q" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "T" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "W" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 11.15, per 1000 atoms: 0.18 Number of scatterers: 62387 At special positions: 0 Unit cell: (161.564, 161.564, 161.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 480 16.00 O 12899 8.00 N 10080 7.00 C 38904 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: 10.53 Conformation dependent library (CDL) restraints added in 5.5 seconds 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13680 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 24 sheets defined 43.5% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.789A pdb=" N HIS A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE A 149 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.791A pdb=" N ILE A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE B 149 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE C 149 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 132 through 143 Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE D 149 " --> pdb=" O ALA D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 279 " --> pdb=" O GLN D 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU E 20 " --> pdb=" O ASP E 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS E 86 " --> pdb=" O ASN E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE E 149 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 187 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 213 through 223 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE E 276 " --> pdb=" O GLU E 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 280 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 Processing helix chain 'F' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS F 86 " --> pdb=" O ASN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE F 149 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 213 through 223 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 265 through 270 Processing helix chain 'F' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE F 276 " --> pdb=" O GLU F 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 35 Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS G 86 " --> pdb=" O ASN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 102 Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE G 149 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 187 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 213 through 223 Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 265 through 270 Processing helix chain 'G' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE G 276 " --> pdb=" O GLU G 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL G 280 " --> pdb=" O ILE G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 308 Processing helix chain 'H' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU H 20 " --> pdb=" O ASP H 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 35 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS H 86 " --> pdb=" O ASN H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 102 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE H 149 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 187 Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'H' and resid 213 through 223 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS H 279 " --> pdb=" O GLN H 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 280 " --> pdb=" O ILE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 308 Processing helix chain 'I' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU I 20 " --> pdb=" O ASP I 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 35 Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 102 Processing helix chain 'I' and resid 103 through 105 No H-bonds generated for 'chain 'I' and resid 103 through 105' Processing helix chain 'I' and resid 132 through 143 Processing helix chain 'I' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE I 149 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 187 Processing helix chain 'I' and resid 188 through 190 No H-bonds generated for 'chain 'I' and resid 188 through 190' Processing helix chain 'I' and resid 213 through 223 Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 256 through 265 Processing helix chain 'I' and resid 265 through 270 Processing helix chain 'I' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE I 276 " --> pdb=" O GLU I 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS I 279 " --> pdb=" O GLN I 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I 280 " --> pdb=" O ILE I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 308 Processing helix chain 'J' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 35 Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS J 86 " --> pdb=" O ASN J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 102 Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 132 through 143 Processing helix chain 'J' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE J 149 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 187 Processing helix chain 'J' and resid 188 through 190 No H-bonds generated for 'chain 'J' and resid 188 through 190' Processing helix chain 'J' and resid 213 through 223 Processing helix chain 'J' and resid 237 through 241 Processing helix chain 'J' and resid 256 through 265 Processing helix chain 'J' and resid 265 through 270 Processing helix chain 'J' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE J 276 " --> pdb=" O GLU J 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS J 279 " --> pdb=" O GLN J 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL J 280 " --> pdb=" O ILE J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 308 Processing helix chain 'K' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 35 Processing helix chain 'K' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS K 86 " --> pdb=" O ASN K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 132 through 143 Processing helix chain 'K' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE K 149 " --> pdb=" O ALA K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 187 Processing helix chain 'K' and resid 188 through 190 No H-bonds generated for 'chain 'K' and resid 188 through 190' Processing helix chain 'K' and resid 213 through 223 Processing helix chain 'K' and resid 237 through 241 Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'K' and resid 265 through 270 Processing helix chain 'K' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS K 279 " --> pdb=" O GLN K 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL K 280 " --> pdb=" O ILE K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 308 Processing helix chain 'L' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU L 20 " --> pdb=" O ASP L 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 35 Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS L 86 " --> pdb=" O ASN L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 102 Processing helix chain 'L' and resid 103 through 105 No H-bonds generated for 'chain 'L' and resid 103 through 105' Processing helix chain 'L' and resid 132 through 143 Processing helix chain 'L' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE L 149 " --> pdb=" O ALA L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 187 Processing helix chain 'L' and resid 188 through 190 No H-bonds generated for 'chain 'L' and resid 188 through 190' Processing helix chain 'L' and resid 213 through 223 Processing helix chain 'L' and resid 237 through 241 Processing helix chain 'L' and resid 256 through 265 Processing helix chain 'L' and resid 265 through 270 Processing helix chain 'L' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE L 276 " --> pdb=" O GLU L 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS L 279 " --> pdb=" O GLN L 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL L 280 " --> pdb=" O ILE L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 308 Processing helix chain 'M' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU M 20 " --> pdb=" O ASP M 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 35 Processing helix chain 'M' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS M 86 " --> pdb=" O ASN M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 102 Processing helix chain 'M' and resid 103 through 105 No H-bonds generated for 'chain 'M' and resid 103 through 105' Processing helix chain 'M' and resid 132 through 143 Processing helix chain 'M' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE M 149 " --> pdb=" O ALA M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 187 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 213 through 223 Processing helix chain 'M' and resid 237 through 241 Processing helix chain 'M' and resid 256 through 265 Processing helix chain 'M' and resid 265 through 270 Processing helix chain 'M' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS M 279 " --> pdb=" O GLN M 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL M 280 " --> pdb=" O ILE M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 308 Processing helix chain 'N' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 35 Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS N 86 " --> pdb=" O ASN N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 102 Processing helix chain 'N' and resid 103 through 105 No H-bonds generated for 'chain 'N' and resid 103 through 105' Processing helix chain 'N' and resid 132 through 143 Processing helix chain 'N' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE N 149 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 187 Processing helix chain 'N' and resid 188 through 190 No H-bonds generated for 'chain 'N' and resid 188 through 190' Processing helix chain 'N' and resid 213 through 223 Processing helix chain 'N' and resid 237 through 241 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 265 through 270 Processing helix chain 'N' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE N 276 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS N 279 " --> pdb=" O GLN N 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL N 280 " --> pdb=" O ILE N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 308 Processing helix chain 'O' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU O 20 " --> pdb=" O ASP O 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 35 Processing helix chain 'O' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS O 86 " --> pdb=" O ASN O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 102 Processing helix chain 'O' and resid 103 through 105 No H-bonds generated for 'chain 'O' and resid 103 through 105' Processing helix chain 'O' and resid 132 through 143 Processing helix chain 'O' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE O 149 " --> pdb=" O ALA O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 187 Processing helix chain 'O' and resid 188 through 190 No H-bonds generated for 'chain 'O' and resid 188 through 190' Processing helix chain 'O' and resid 213 through 223 Processing helix chain 'O' and resid 237 through 241 Processing helix chain 'O' and resid 256 through 265 Processing helix chain 'O' and resid 265 through 270 Processing helix chain 'O' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE O 276 " --> pdb=" O GLU O 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS O 279 " --> pdb=" O GLN O 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL O 280 " --> pdb=" O ILE O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 308 Processing helix chain 'P' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU P 20 " --> pdb=" O ASP P 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS P 86 " --> pdb=" O ASN P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 102 Processing helix chain 'P' and resid 103 through 105 No H-bonds generated for 'chain 'P' and resid 103 through 105' Processing helix chain 'P' and resid 132 through 143 Processing helix chain 'P' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE P 149 " --> pdb=" O ALA P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 187 Processing helix chain 'P' and resid 188 through 190 No H-bonds generated for 'chain 'P' and resid 188 through 190' Processing helix chain 'P' and resid 213 through 223 Processing helix chain 'P' and resid 237 through 241 Processing helix chain 'P' and resid 256 through 265 Processing helix chain 'P' and resid 265 through 270 Processing helix chain 'P' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE P 276 " --> pdb=" O GLU P 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS P 279 " --> pdb=" O GLN P 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL P 280 " --> pdb=" O ILE P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 308 Processing helix chain 'Q' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU Q 20 " --> pdb=" O ASP Q 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY Q 24 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS Q 86 " --> pdb=" O ASN Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 102 Processing helix chain 'Q' and resid 103 through 105 No H-bonds generated for 'chain 'Q' and resid 103 through 105' Processing helix chain 'Q' and resid 132 through 143 Processing helix chain 'Q' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE Q 149 " --> pdb=" O ALA Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 187 Processing helix chain 'Q' and resid 188 through 190 No H-bonds generated for 'chain 'Q' and resid 188 through 190' Processing helix chain 'Q' and resid 213 through 223 Processing helix chain 'Q' and resid 237 through 241 Processing helix chain 'Q' and resid 256 through 265 Processing helix chain 'Q' and resid 265 through 270 Processing helix chain 'Q' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE Q 276 " --> pdb=" O GLU Q 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS Q 279 " --> pdb=" O GLN Q 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL Q 280 " --> pdb=" O ILE Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 308 Processing helix chain 'R' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 35 Processing helix chain 'R' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS R 86 " --> pdb=" O ASN R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 102 Processing helix chain 'R' and resid 103 through 105 No H-bonds generated for 'chain 'R' and resid 103 through 105' Processing helix chain 'R' and resid 132 through 143 Processing helix chain 'R' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE R 149 " --> pdb=" O ALA R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 187 Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 237 through 241 Processing helix chain 'R' and resid 256 through 265 Processing helix chain 'R' and resid 265 through 270 Processing helix chain 'R' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE R 276 " --> pdb=" O GLU R 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS R 279 " --> pdb=" O GLN R 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 308 Processing helix chain 'S' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU S 20 " --> pdb=" O ASP S 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY S 24 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 35 Processing helix chain 'S' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS S 86 " --> pdb=" O ASN S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 102 Processing helix chain 'S' and resid 103 through 105 No H-bonds generated for 'chain 'S' and resid 103 through 105' Processing helix chain 'S' and resid 132 through 143 Processing helix chain 'S' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE S 149 " --> pdb=" O ALA S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 187 Processing helix chain 'S' and resid 188 through 190 No H-bonds generated for 'chain 'S' and resid 188 through 190' Processing helix chain 'S' and resid 213 through 223 Processing helix chain 'S' and resid 237 through 241 Processing helix chain 'S' and resid 256 through 265 Processing helix chain 'S' and resid 265 through 270 Processing helix chain 'S' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE S 276 " --> pdb=" O GLU S 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS S 279 " --> pdb=" O GLN S 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL S 280 " --> pdb=" O ILE S 276 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 308 Processing helix chain 'T' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU T 20 " --> pdb=" O ASP T 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY T 24 " --> pdb=" O LEU T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 35 Processing helix chain 'T' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS T 86 " --> pdb=" O ASN T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 102 Processing helix chain 'T' and resid 103 through 105 No H-bonds generated for 'chain 'T' and resid 103 through 105' Processing helix chain 'T' and resid 132 through 143 Processing helix chain 'T' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE T 149 " --> pdb=" O ALA T 146 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 187 Processing helix chain 'T' and resid 188 through 190 No H-bonds generated for 'chain 'T' and resid 188 through 190' Processing helix chain 'T' and resid 213 through 223 Processing helix chain 'T' and resid 237 through 241 Processing helix chain 'T' and resid 256 through 265 Processing helix chain 'T' and resid 265 through 270 Processing helix chain 'T' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE T 276 " --> pdb=" O GLU T 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS T 279 " --> pdb=" O GLN T 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL T 280 " --> pdb=" O ILE T 276 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 308 Processing helix chain 'U' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU U 20 " --> pdb=" O ASP U 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 35 Processing helix chain 'U' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS U 86 " --> pdb=" O ASN U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 102 Processing helix chain 'U' and resid 103 through 105 No H-bonds generated for 'chain 'U' and resid 103 through 105' Processing helix chain 'U' and resid 132 through 143 Processing helix chain 'U' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE U 149 " --> pdb=" O ALA U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 187 Processing helix chain 'U' and resid 188 through 190 No H-bonds generated for 'chain 'U' and resid 188 through 190' Processing helix chain 'U' and resid 213 through 223 Processing helix chain 'U' and resid 237 through 241 Processing helix chain 'U' and resid 256 through 265 Processing helix chain 'U' and resid 265 through 270 Processing helix chain 'U' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE U 276 " --> pdb=" O GLU U 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS U 279 " --> pdb=" O GLN U 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL U 280 " --> pdb=" O ILE U 276 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 308 Processing helix chain 'V' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU V 20 " --> pdb=" O ASP V 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 35 Processing helix chain 'V' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS V 86 " --> pdb=" O ASN V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 102 Processing helix chain 'V' and resid 103 through 105 No H-bonds generated for 'chain 'V' and resid 103 through 105' Processing helix chain 'V' and resid 132 through 143 Processing helix chain 'V' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE V 149 " --> pdb=" O ALA V 146 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 187 Processing helix chain 'V' and resid 188 through 190 No H-bonds generated for 'chain 'V' and resid 188 through 190' Processing helix chain 'V' and resid 213 through 223 Processing helix chain 'V' and resid 237 through 241 Processing helix chain 'V' and resid 256 through 265 Processing helix chain 'V' and resid 265 through 270 Processing helix chain 'V' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE V 276 " --> pdb=" O GLU V 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS V 279 " --> pdb=" O GLN V 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL V 280 " --> pdb=" O ILE V 276 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 308 Processing helix chain 'W' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU W 20 " --> pdb=" O ASP W 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY W 24 " --> pdb=" O LEU W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 35 Processing helix chain 'W' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS W 86 " --> pdb=" O ASN W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 102 Processing helix chain 'W' and resid 103 through 105 No H-bonds generated for 'chain 'W' and resid 103 through 105' Processing helix chain 'W' and resid 132 through 143 Processing helix chain 'W' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE W 149 " --> pdb=" O ALA W 146 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 187 Processing helix chain 'W' and resid 188 through 190 No H-bonds generated for 'chain 'W' and resid 188 through 190' Processing helix chain 'W' and resid 213 through 223 Processing helix chain 'W' and resid 237 through 241 Processing helix chain 'W' and resid 256 through 265 Processing helix chain 'W' and resid 265 through 270 Processing helix chain 'W' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE W 276 " --> pdb=" O GLU W 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS W 279 " --> pdb=" O GLN W 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL W 280 " --> pdb=" O ILE W 276 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 308 Processing helix chain 'X' and resid 16 through 26 removed outlier: 3.592A pdb=" N LEU X 20 " --> pdb=" O ASP X 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY X 24 " --> pdb=" O LEU X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 Processing helix chain 'X' and resid 82 through 93 removed outlier: 3.788A pdb=" N HIS X 86 " --> pdb=" O ASN X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 102 Processing helix chain 'X' and resid 103 through 105 No H-bonds generated for 'chain 'X' and resid 103 through 105' Processing helix chain 'X' and resid 132 through 143 Processing helix chain 'X' and resid 145 through 149 removed outlier: 3.507A pdb=" N ILE X 149 " --> pdb=" O ALA X 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 187 Processing helix chain 'X' and resid 188 through 190 No H-bonds generated for 'chain 'X' and resid 188 through 190' Processing helix chain 'X' and resid 213 through 223 Processing helix chain 'X' and resid 237 through 241 Processing helix chain 'X' and resid 256 through 265 Processing helix chain 'X' and resid 265 through 270 Processing helix chain 'X' and resid 270 through 282 removed outlier: 3.792A pdb=" N ILE X 276 " --> pdb=" O GLU X 272 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS X 279 " --> pdb=" O GLN X 275 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL X 280 " --> pdb=" O ILE X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU A 12 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY A 111 " --> pdb=" O MET A 10 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N MET A 10 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR A 113 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 8 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 203 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU A 118 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 201 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 120 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU A 199 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 122 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET A 197 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 195 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG A 247 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 167 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY A 287 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG A 291 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 51 " --> pdb=" O ARG A 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU A 293 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 49 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 47 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 297 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 42 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET A 73 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLY A 50 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 12.384A pdb=" N SER A 71 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU B 12 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY B 111 " --> pdb=" O MET B 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET B 10 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B 113 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 8 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 203 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B 118 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU B 201 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 120 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 199 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 122 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET B 197 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 195 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG B 247 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 167 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY B 287 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG B 291 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 51 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 293 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE B 49 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 47 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 297 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 42 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET B 73 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY B 50 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER B 71 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU C 12 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY C 111 " --> pdb=" O MET C 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET C 10 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 113 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE C 8 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 203 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU C 118 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU C 201 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 120 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU C 199 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA C 122 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET C 197 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 195 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG C 247 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE C 167 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY C 287 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG C 291 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 51 " --> pdb=" O ARG C 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU C 293 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 49 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C 47 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET C 297 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 42 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET C 73 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY C 50 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER C 71 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU D 12 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY D 111 " --> pdb=" O MET D 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET D 10 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR D 113 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE D 8 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 203 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU D 118 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU D 201 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 120 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU D 199 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 122 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET D 197 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY D 195 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG D 247 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 167 " --> pdb=" O GLY D 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY D 287 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 291 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 51 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU D 293 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE D 49 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL D 47 " --> pdb=" O PRO D 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET D 297 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY D 42 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET D 73 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY D 50 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER D 71 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU E 12 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY E 111 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET E 10 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR E 113 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE E 8 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY E 203 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU E 118 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU E 201 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL E 120 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU E 199 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA E 122 " --> pdb=" O MET E 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET E 197 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 195 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG E 247 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE E 167 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY E 287 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG E 291 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 51 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 293 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE E 49 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL E 47 " --> pdb=" O PRO E 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET E 297 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY E 42 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET E 73 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY E 50 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER E 71 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU F 12 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY F 111 " --> pdb=" O MET F 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET F 10 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR F 113 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE F 8 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY F 203 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU F 118 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU F 201 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 120 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU F 199 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA F 122 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET F 197 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 195 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG F 247 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 167 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY F 287 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG F 291 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL F 51 " --> pdb=" O ARG F 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU F 293 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE F 49 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL F 47 " --> pdb=" O PRO F 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET F 297 " --> pdb=" O ASN F 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 42 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET F 73 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY F 50 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER F 71 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU G 12 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY G 111 " --> pdb=" O MET G 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET G 10 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR G 113 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE G 8 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY G 203 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU G 118 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU G 201 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL G 120 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU G 199 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA G 122 " --> pdb=" O MET G 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET G 197 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY G 195 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG G 247 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE G 167 " --> pdb=" O GLY G 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY G 287 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG G 291 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL G 51 " --> pdb=" O ARG G 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU G 293 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE G 49 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL G 47 " --> pdb=" O PRO G 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET G 297 " --> pdb=" O ASN G 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY G 42 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET G 73 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY G 50 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER G 71 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU H 12 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY H 111 " --> pdb=" O MET H 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET H 10 " --> pdb=" O GLY H 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR H 113 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE H 8 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY H 203 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU H 118 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU H 201 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL H 120 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU H 199 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA H 122 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET H 197 " --> pdb=" O ALA H 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY H 195 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG H 247 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE H 167 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY H 287 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG H 291 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL H 51 " --> pdb=" O ARG H 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU H 293 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE H 49 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL H 47 " --> pdb=" O PRO H 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET H 297 " --> pdb=" O ASN H 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY H 42 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET H 73 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY H 50 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER H 71 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU I 12 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY I 111 " --> pdb=" O MET I 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET I 10 " --> pdb=" O GLY I 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR I 113 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE I 8 " --> pdb=" O TYR I 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY I 203 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU I 118 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU I 201 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL I 120 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU I 199 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA I 122 " --> pdb=" O MET I 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET I 197 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY I 195 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG I 247 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE I 167 " --> pdb=" O GLY I 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY I 287 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG I 291 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL I 51 " --> pdb=" O ARG I 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU I 293 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE I 49 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL I 47 " --> pdb=" O PRO I 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET I 297 " --> pdb=" O ASN I 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY I 42 " --> pdb=" O PHE I 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET I 73 " --> pdb=" O GLN I 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY I 50 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER I 71 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU J 12 " --> pdb=" O ILE J 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY J 111 " --> pdb=" O MET J 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET J 10 " --> pdb=" O GLY J 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR J 113 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE J 8 " --> pdb=" O TYR J 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY J 203 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU J 118 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU J 201 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL J 120 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU J 199 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA J 122 " --> pdb=" O MET J 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET J 197 " --> pdb=" O ALA J 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY J 195 " --> pdb=" O GLU J 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG J 247 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE J 167 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY J 287 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG J 291 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL J 51 " --> pdb=" O ARG J 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU J 293 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE J 49 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL J 47 " --> pdb=" O PRO J 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET J 297 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY J 42 " --> pdb=" O PHE J 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET J 73 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY J 50 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER J 71 " --> pdb=" O GLY J 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU K 12 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY K 111 " --> pdb=" O MET K 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET K 10 " --> pdb=" O GLY K 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR K 113 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE K 8 " --> pdb=" O TYR K 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY K 203 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU K 118 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU K 201 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL K 120 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU K 199 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA K 122 " --> pdb=" O MET K 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET K 197 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY K 195 " --> pdb=" O GLU K 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG K 247 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE K 167 " --> pdb=" O GLY K 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY K 287 " --> pdb=" O ILE K 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 291 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL K 51 " --> pdb=" O ARG K 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU K 293 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE K 49 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL K 47 " --> pdb=" O PRO K 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET K 297 " --> pdb=" O ASN K 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY K 42 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET K 73 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY K 50 " --> pdb=" O SER K 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER K 71 " --> pdb=" O GLY K 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU L 12 " --> pdb=" O ILE L 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY L 111 " --> pdb=" O MET L 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET L 10 " --> pdb=" O GLY L 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR L 113 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE L 8 " --> pdb=" O TYR L 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY L 203 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU L 118 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU L 201 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL L 120 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU L 199 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA L 122 " --> pdb=" O MET L 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET L 197 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY L 195 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG L 247 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE L 167 " --> pdb=" O GLY L 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY L 287 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG L 291 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL L 51 " --> pdb=" O ARG L 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU L 293 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE L 49 " --> pdb=" O LEU L 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL L 47 " --> pdb=" O PRO L 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET L 297 " --> pdb=" O ASN L 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY L 42 " --> pdb=" O PHE L 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET L 73 " --> pdb=" O GLN L 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY L 50 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER L 71 " --> pdb=" O GLY L 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU M 12 " --> pdb=" O ILE M 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY M 111 " --> pdb=" O MET M 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET M 10 " --> pdb=" O GLY M 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR M 113 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE M 8 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY M 203 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU M 118 " --> pdb=" O GLU M 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU M 201 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL M 120 " --> pdb=" O LEU M 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU M 199 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA M 122 " --> pdb=" O MET M 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET M 197 " --> pdb=" O ALA M 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY M 195 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG M 247 " --> pdb=" O GLU M 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE M 167 " --> pdb=" O GLY M 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY M 287 " --> pdb=" O ILE M 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG M 291 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL M 51 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU M 293 " --> pdb=" O ILE M 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE M 49 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL M 47 " --> pdb=" O PRO M 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET M 297 " --> pdb=" O ASN M 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY M 42 " --> pdb=" O PHE M 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET M 73 " --> pdb=" O GLN M 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY M 50 " --> pdb=" O SER M 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER M 71 " --> pdb=" O GLY M 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU N 12 " --> pdb=" O ILE N 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY N 111 " --> pdb=" O MET N 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET N 10 " --> pdb=" O GLY N 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR N 113 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE N 8 " --> pdb=" O TYR N 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 203 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU N 118 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU N 201 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL N 120 " --> pdb=" O LEU N 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU N 199 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA N 122 " --> pdb=" O MET N 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET N 197 " --> pdb=" O ALA N 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY N 195 " --> pdb=" O GLU N 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG N 247 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE N 167 " --> pdb=" O GLY N 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY N 287 " --> pdb=" O ILE N 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG N 291 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL N 51 " --> pdb=" O ARG N 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU N 293 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE N 49 " --> pdb=" O LEU N 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL N 47 " --> pdb=" O PRO N 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET N 297 " --> pdb=" O ASN N 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY N 42 " --> pdb=" O PHE N 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET N 73 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY N 50 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER N 71 " --> pdb=" O GLY N 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU O 12 " --> pdb=" O ILE O 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY O 111 " --> pdb=" O MET O 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET O 10 " --> pdb=" O GLY O 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR O 113 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE O 8 " --> pdb=" O TYR O 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY O 203 " --> pdb=" O LEU O 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU O 118 " --> pdb=" O GLU O 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU O 201 " --> pdb=" O GLU O 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL O 120 " --> pdb=" O LEU O 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU O 199 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA O 122 " --> pdb=" O MET O 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET O 197 " --> pdb=" O ALA O 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY O 195 " --> pdb=" O GLU O 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG O 247 " --> pdb=" O GLU O 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE O 167 " --> pdb=" O GLY O 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY O 287 " --> pdb=" O ILE O 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG O 291 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL O 51 " --> pdb=" O ARG O 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU O 293 " --> pdb=" O ILE O 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE O 49 " --> pdb=" O LEU O 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL O 47 " --> pdb=" O PRO O 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET O 297 " --> pdb=" O ASN O 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY O 42 " --> pdb=" O PHE O 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET O 73 " --> pdb=" O GLN O 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY O 50 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER O 71 " --> pdb=" O GLY O 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU P 12 " --> pdb=" O ILE P 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY P 111 " --> pdb=" O MET P 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET P 10 " --> pdb=" O GLY P 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR P 113 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE P 8 " --> pdb=" O TYR P 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY P 203 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU P 118 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU P 201 " --> pdb=" O GLU P 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL P 120 " --> pdb=" O LEU P 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU P 199 " --> pdb=" O VAL P 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA P 122 " --> pdb=" O MET P 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET P 197 " --> pdb=" O ALA P 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 195 " --> pdb=" O GLU P 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG P 247 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE P 167 " --> pdb=" O GLY P 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY P 287 " --> pdb=" O ILE P 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG P 291 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL P 51 " --> pdb=" O ARG P 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU P 293 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE P 49 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL P 47 " --> pdb=" O PRO P 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET P 297 " --> pdb=" O ASN P 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY P 42 " --> pdb=" O PHE P 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET P 73 " --> pdb=" O GLN P 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY P 50 " --> pdb=" O SER P 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER P 71 " --> pdb=" O GLY P 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU Q 12 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY Q 111 " --> pdb=" O MET Q 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET Q 10 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR Q 113 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE Q 8 " --> pdb=" O TYR Q 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY Q 203 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU Q 118 " --> pdb=" O GLU Q 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU Q 201 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL Q 120 " --> pdb=" O LEU Q 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU Q 199 " --> pdb=" O VAL Q 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA Q 122 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET Q 197 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY Q 195 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG Q 247 " --> pdb=" O GLU Q 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE Q 167 " --> pdb=" O GLY Q 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY Q 287 " --> pdb=" O ILE Q 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG Q 291 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL Q 51 " --> pdb=" O ARG Q 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU Q 293 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE Q 49 " --> pdb=" O LEU Q 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET Q 297 " --> pdb=" O ASN Q 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY Q 42 " --> pdb=" O PHE Q 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET Q 73 " --> pdb=" O GLN Q 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY Q 50 " --> pdb=" O SER Q 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER Q 71 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU R 12 " --> pdb=" O ILE R 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY R 111 " --> pdb=" O MET R 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET R 10 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR R 113 " --> pdb=" O ILE R 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE R 8 " --> pdb=" O TYR R 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY R 203 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU R 118 " --> pdb=" O GLU R 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU R 201 " --> pdb=" O GLU R 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL R 120 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU R 199 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA R 122 " --> pdb=" O MET R 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET R 197 " --> pdb=" O ALA R 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY R 195 " --> pdb=" O GLU R 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG R 247 " --> pdb=" O GLU R 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE R 167 " --> pdb=" O GLY R 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY R 287 " --> pdb=" O ILE R 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG R 291 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL R 51 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU R 293 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE R 49 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL R 47 " --> pdb=" O PRO R 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET R 297 " --> pdb=" O ASN R 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY R 42 " --> pdb=" O PHE R 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET R 73 " --> pdb=" O GLN R 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY R 50 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER R 71 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU S 12 " --> pdb=" O ILE S 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY S 111 " --> pdb=" O MET S 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET S 10 " --> pdb=" O GLY S 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR S 113 " --> pdb=" O ILE S 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE S 8 " --> pdb=" O TYR S 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY S 203 " --> pdb=" O LEU S 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU S 118 " --> pdb=" O GLU S 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU S 201 " --> pdb=" O GLU S 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL S 120 " --> pdb=" O LEU S 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU S 199 " --> pdb=" O VAL S 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA S 122 " --> pdb=" O MET S 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET S 197 " --> pdb=" O ALA S 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY S 195 " --> pdb=" O GLU S 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG S 247 " --> pdb=" O GLU S 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE S 167 " --> pdb=" O GLY S 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY S 287 " --> pdb=" O ILE S 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG S 291 " --> pdb=" O VAL S 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL S 51 " --> pdb=" O ARG S 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU S 293 " --> pdb=" O ILE S 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE S 49 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL S 47 " --> pdb=" O PRO S 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET S 297 " --> pdb=" O ASN S 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY S 42 " --> pdb=" O PHE S 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET S 73 " --> pdb=" O GLN S 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY S 50 " --> pdb=" O SER S 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER S 71 " --> pdb=" O GLY S 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU T 12 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY T 111 " --> pdb=" O MET T 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET T 10 " --> pdb=" O GLY T 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR T 113 " --> pdb=" O ILE T 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE T 8 " --> pdb=" O TYR T 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY T 203 " --> pdb=" O LEU T 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU T 118 " --> pdb=" O GLU T 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU T 201 " --> pdb=" O GLU T 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL T 120 " --> pdb=" O LEU T 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU T 199 " --> pdb=" O VAL T 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA T 122 " --> pdb=" O MET T 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET T 197 " --> pdb=" O ALA T 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY T 195 " --> pdb=" O GLU T 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG T 247 " --> pdb=" O GLU T 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE T 167 " --> pdb=" O GLY T 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY T 287 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG T 291 " --> pdb=" O VAL T 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL T 51 " --> pdb=" O ARG T 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU T 293 " --> pdb=" O ILE T 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE T 49 " --> pdb=" O LEU T 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL T 47 " --> pdb=" O PRO T 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET T 297 " --> pdb=" O ASN T 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY T 42 " --> pdb=" O PHE T 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET T 73 " --> pdb=" O GLN T 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY T 50 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER T 71 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU U 12 " --> pdb=" O ILE U 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY U 111 " --> pdb=" O MET U 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET U 10 " --> pdb=" O GLY U 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR U 113 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE U 8 " --> pdb=" O TYR U 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY U 203 " --> pdb=" O LEU U 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU U 118 " --> pdb=" O GLU U 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU U 201 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL U 120 " --> pdb=" O LEU U 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU U 199 " --> pdb=" O VAL U 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA U 122 " --> pdb=" O MET U 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET U 197 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY U 195 " --> pdb=" O GLU U 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG U 247 " --> pdb=" O GLU U 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE U 167 " --> pdb=" O GLY U 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY U 287 " --> pdb=" O ILE U 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG U 291 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL U 51 " --> pdb=" O ARG U 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU U 293 " --> pdb=" O ILE U 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE U 49 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL U 47 " --> pdb=" O PRO U 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET U 297 " --> pdb=" O ASN U 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY U 42 " --> pdb=" O PHE U 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET U 73 " --> pdb=" O GLN U 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY U 50 " --> pdb=" O SER U 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER U 71 " --> pdb=" O GLY U 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU V 12 " --> pdb=" O ILE V 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY V 111 " --> pdb=" O MET V 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET V 10 " --> pdb=" O GLY V 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR V 113 " --> pdb=" O ILE V 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE V 8 " --> pdb=" O TYR V 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY V 203 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU V 118 " --> pdb=" O GLU V 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU V 201 " --> pdb=" O GLU V 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL V 120 " --> pdb=" O LEU V 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU V 199 " --> pdb=" O VAL V 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA V 122 " --> pdb=" O MET V 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET V 197 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY V 195 " --> pdb=" O GLU V 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG V 247 " --> pdb=" O GLU V 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE V 167 " --> pdb=" O GLY V 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY V 287 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG V 291 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL V 51 " --> pdb=" O ARG V 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU V 293 " --> pdb=" O ILE V 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE V 49 " --> pdb=" O LEU V 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL V 47 " --> pdb=" O PRO V 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET V 297 " --> pdb=" O ASN V 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY V 42 " --> pdb=" O PHE V 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET V 73 " --> pdb=" O GLN V 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY V 50 " --> pdb=" O SER V 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER V 71 " --> pdb=" O GLY V 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU W 12 " --> pdb=" O ILE W 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY W 111 " --> pdb=" O MET W 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET W 10 " --> pdb=" O GLY W 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR W 113 " --> pdb=" O ILE W 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE W 8 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY W 203 " --> pdb=" O LEU W 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU W 118 " --> pdb=" O GLU W 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU W 201 " --> pdb=" O GLU W 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL W 120 " --> pdb=" O LEU W 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU W 199 " --> pdb=" O VAL W 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA W 122 " --> pdb=" O MET W 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET W 197 " --> pdb=" O ALA W 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY W 195 " --> pdb=" O GLU W 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG W 247 " --> pdb=" O GLU W 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE W 167 " --> pdb=" O GLY W 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY W 287 " --> pdb=" O ILE W 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG W 291 " --> pdb=" O VAL W 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL W 51 " --> pdb=" O ARG W 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU W 293 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE W 49 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL W 47 " --> pdb=" O PRO W 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET W 297 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY W 42 " --> pdb=" O PHE W 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET W 73 " --> pdb=" O GLN W 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY W 50 " --> pdb=" O SER W 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER W 71 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 108 through 113 removed outlier: 6.506A pdb=" N GLU X 12 " --> pdb=" O ILE X 109 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY X 111 " --> pdb=" O MET X 10 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N MET X 10 " --> pdb=" O GLY X 111 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR X 113 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE X 8 " --> pdb=" O TYR X 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY X 203 " --> pdb=" O LEU X 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU X 118 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU X 201 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL X 120 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU X 199 " --> pdb=" O VAL X 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA X 122 " --> pdb=" O MET X 197 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET X 197 " --> pdb=" O ALA X 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY X 195 " --> pdb=" O GLU X 253 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG X 247 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE X 167 " --> pdb=" O GLY X 287 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY X 287 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG X 291 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL X 51 " --> pdb=" O ARG X 291 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU X 293 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE X 49 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL X 47 " --> pdb=" O PRO X 295 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET X 297 " --> pdb=" O ASN X 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY X 42 " --> pdb=" O PHE X 79 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET X 73 " --> pdb=" O GLN X 48 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY X 50 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 12.383A pdb=" N SER X 71 " --> pdb=" O GLY X 50 " (cutoff:3.500A) 2784 hydrogen bonds defined for protein. 7920 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: 24.86 Time building geometry restraints manager: 12.73 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: 18549 1.34 - 1.46: 11138 1.46 - 1.57: 31297 1.57 - 1.69: 0 1.69 - 1.81: 888 Bond restraints: 61872 Sorted by residual: bond pdb=" CB PRO A 245 " pdb=" CG PRO A 245 " ideal model delta sigma weight residual 1.506 1.446 0.060 3.90e-02 6.57e+02 2.39e+00 bond pdb=" CB PRO F 245 " pdb=" CG PRO F 245 " ideal model delta sigma weight residual 1.506 1.447 0.059 3.90e-02 6.57e+02 2.32e+00 bond pdb=" CB PRO G 245 " pdb=" CG PRO G 245 " ideal model delta sigma weight residual 1.506 1.447 0.059 3.90e-02 6.57e+02 2.32e+00 bond pdb=" CB PRO Q 245 " pdb=" CG PRO Q 245 " ideal model delta sigma weight residual 1.506 1.447 0.059 3.90e-02 6.57e+02 2.32e+00 bond pdb=" CB PRO T 245 " pdb=" CG PRO T 245 " ideal model delta sigma weight residual 1.506 1.447 0.059 3.90e-02 6.57e+02 2.32e+00 ... (remaining 61867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 81144 1.96 - 3.92: 2448 3.92 - 5.87: 240 5.87 - 7.83: 96 7.83 - 9.79: 24 Bond angle restraints: 83952 Sorted by residual: angle pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " pdb=" CG TYR A 77 " ideal model delta sigma weight residual 113.90 120.07 -6.17 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR I 77 " pdb=" CB TYR I 77 " pdb=" CG TYR I 77 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR U 77 " pdb=" CB TYR U 77 " pdb=" CG TYR U 77 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR S 77 " pdb=" CB TYR S 77 " pdb=" CG TYR S 77 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR R 77 " pdb=" CB TYR R 77 " pdb=" CG TYR R 77 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 ... (remaining 83947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 32496 15.87 - 31.74: 3216 31.74 - 47.61: 672 47.61 - 63.48: 144 63.48 - 79.35: 144 Dihedral angle restraints: 36672 sinusoidal: 15216 harmonic: 21456 Sorted by residual: dihedral pdb=" CA ARG A 57 " pdb=" C ARG A 57 " pdb=" N TRP A 58 " pdb=" CA TRP A 58 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG B 57 " pdb=" C ARG B 57 " pdb=" N TRP B 58 " pdb=" CA TRP B 58 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ARG V 57 " pdb=" C ARG V 57 " pdb=" N TRP V 58 " pdb=" CA TRP V 58 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 36669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4703 0.038 - 0.076: 2713 0.076 - 0.114: 1151 0.114 - 0.152: 194 0.152 - 0.190: 47 Chirality restraints: 8808 Sorted by residual: chirality pdb=" CA VAL I 51 " pdb=" N VAL I 51 " pdb=" C VAL I 51 " pdb=" CB VAL I 51 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA VAL F 51 " pdb=" N VAL F 51 " pdb=" C VAL F 51 " pdb=" CB VAL F 51 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA VAL P 51 " pdb=" N VAL P 51 " pdb=" C VAL P 51 " pdb=" CB VAL P 51 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 8805 not shown) Planarity restraints: 10824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 16 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 17 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 16 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO G 17 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 16 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO N 17 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO N 17 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 17 " -0.029 5.00e-02 4.00e+02 ... (remaining 10821 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8999 2.76 - 3.29: 57106 3.29 - 3.83: 123605 3.83 - 4.36: 153747 4.36 - 4.90: 241760 Nonbonded interactions: 585217 Sorted by model distance: nonbonded pdb=" NE2 HIS I 86 " pdb="FE FE I 401 " model vdw 2.222 2.340 nonbonded pdb=" NE2 HIS W 86 " pdb="FE FE W 401 " model vdw 2.222 2.340 nonbonded pdb=" NE2 HIS J 86 " pdb="FE FE J 401 " model vdw 2.222 2.340 nonbonded pdb=" NE2 HIS P 86 " pdb="FE FE P 401 " model vdw 2.222 2.340 nonbonded pdb=" NE2 HIS C 86 " pdb="FE FE C 401 " model vdw 2.222 2.340 ... (remaining 585212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 11.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.910 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 90.930 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 0.060 61872 Z= 0.412 Angle : 0.814 9.792 83952 Z= 0.443 Chirality : 0.053 0.190 8808 Planarity : 0.006 0.052 10824 Dihedral : 13.947 79.348 22992 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.37 % Allowed : 3.73 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.08), residues: 7392 helix: -3.34 (0.05), residues: 2592 sheet: 0.46 (0.12), residues: 1728 loop : -1.45 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 80 HIS 0.008 0.002 HIS J 251 PHE 0.018 0.003 PHE I 163 TYR 0.023 0.003 TYR F 77 ARG 0.002 0.000 ARG G 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1489 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1465 time to evaluate : 6.251 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 1465 average time/residue: 1.6681 time to fit residues: 3057.7756 Evaluate side-chains 1177 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1177 time to evaluate : 5.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 628 optimal weight: 1.9990 chunk 563 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 380 optimal weight: 1.9990 chunk 301 optimal weight: 10.0000 chunk 583 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 354 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 675 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 96 ASN A 103 GLN A 218 HIS A 251 HIS B 37 HIS B 96 ASN B 103 GLN B 218 HIS B 251 HIS C 37 HIS C 96 ASN C 103 GLN C 218 HIS C 251 HIS D 37 HIS D 96 ASN D 103 GLN D 218 HIS D 251 HIS E 37 HIS E 96 ASN E 103 GLN E 218 HIS E 251 HIS F 37 HIS F 96 ASN F 103 GLN F 218 HIS F 251 HIS G 37 HIS G 96 ASN G 103 GLN G 218 HIS G 251 HIS H 37 HIS H 96 ASN H 103 GLN H 218 HIS H 251 HIS I 37 HIS I 96 ASN I 103 GLN I 218 HIS I 251 HIS J 37 HIS J 96 ASN J 103 GLN J 218 HIS J 251 HIS K 37 HIS K 96 ASN K 103 GLN K 218 HIS K 251 HIS L 37 HIS L 96 ASN L 103 GLN L 218 HIS L 251 HIS M 37 HIS M 96 ASN M 103 GLN M 218 HIS M 251 HIS N 37 HIS N 96 ASN N 103 GLN N 218 HIS N 251 HIS O 37 HIS O 96 ASN O 103 GLN O 218 HIS O 251 HIS P 37 HIS P 96 ASN P 103 GLN P 218 HIS P 251 HIS Q 37 HIS Q 96 ASN Q 103 GLN Q 218 HIS Q 251 HIS R 37 HIS R 96 ASN R 103 GLN R 218 HIS R 251 HIS S 37 HIS S 96 ASN S 103 GLN S 218 HIS S 251 HIS T 37 HIS T 96 ASN T 103 GLN T 218 HIS T 251 HIS U 37 HIS U 96 ASN U 103 GLN U 218 HIS U 251 HIS V 37 HIS V 96 ASN V 103 GLN V 218 HIS V 251 HIS W 37 HIS W 96 ASN W 103 GLN W 218 HIS W 251 HIS X 37 HIS X 96 ASN X 103 GLN X 218 HIS X 251 HIS Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 61872 Z= 0.174 Angle : 0.579 5.864 83952 Z= 0.313 Chirality : 0.045 0.143 8808 Planarity : 0.004 0.036 10824 Dihedral : 6.486 71.363 8112 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.61 % Allowed : 9.34 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.09), residues: 7392 helix: -0.68 (0.09), residues: 2904 sheet: 0.70 (0.13), residues: 1728 loop : -1.20 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 80 HIS 0.006 0.001 HIS H 251 PHE 0.017 0.002 PHE F 176 TYR 0.010 0.001 TYR A 179 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1318 time to evaluate : 5.425 Fit side-chains REVERT: A 310 HIS cc_start: 0.8369 (p-80) cc_final: 0.8144 (p90) REVERT: B 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8120 (p90) REVERT: C 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: D 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8119 (p90) REVERT: E 310 HIS cc_start: 0.8329 (p-80) cc_final: 0.8118 (p90) REVERT: F 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8119 (p90) REVERT: G 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8119 (p90) REVERT: H 310 HIS cc_start: 0.8329 (p-80) cc_final: 0.8118 (p90) REVERT: I 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: J 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8119 (p90) REVERT: K 310 HIS cc_start: 0.8329 (p-80) cc_final: 0.8118 (p90) REVERT: L 310 HIS cc_start: 0.8328 (p-80) cc_final: 0.8118 (p90) REVERT: M 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: N 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8119 (p90) REVERT: O 310 HIS cc_start: 0.8329 (p-80) cc_final: 0.8118 (p90) REVERT: P 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: Q 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8120 (p90) REVERT: R 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: S 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8119 (p90) REVERT: T 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8119 (p90) REVERT: U 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: V 310 HIS cc_start: 0.8330 (p-80) cc_final: 0.8118 (p90) REVERT: W 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8120 (p90) REVERT: X 310 HIS cc_start: 0.8331 (p-80) cc_final: 0.8119 (p90) outliers start: 168 outliers final: 0 residues processed: 1414 average time/residue: 1.6641 time to fit residues: 2950.3570 Evaluate side-chains 1202 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1202 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 375 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 562 optimal weight: 8.9990 chunk 460 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 676 optimal weight: 7.9990 chunk 731 optimal weight: 0.9980 chunk 602 optimal weight: 7.9990 chunk 671 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 542 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 103 GLN A 275 GLN A 310 HIS B 96 ASN B 103 GLN B 275 GLN B 310 HIS C 96 ASN C 103 GLN C 275 GLN C 310 HIS D 96 ASN D 103 GLN D 275 GLN D 310 HIS E 96 ASN E 103 GLN E 275 GLN E 310 HIS F 96 ASN F 103 GLN F 275 GLN F 310 HIS G 96 ASN G 103 GLN G 275 GLN G 310 HIS H 96 ASN H 103 GLN H 275 GLN H 310 HIS I 96 ASN I 103 GLN I 275 GLN I 310 HIS J 96 ASN J 103 GLN J 275 GLN J 310 HIS K 96 ASN K 103 GLN K 275 GLN K 310 HIS L 96 ASN L 103 GLN L 275 GLN L 310 HIS M 96 ASN M 103 GLN M 275 GLN M 310 HIS N 96 ASN N 103 GLN N 275 GLN N 310 HIS O 96 ASN O 103 GLN O 275 GLN O 310 HIS P 96 ASN P 103 GLN P 275 GLN P 310 HIS Q 96 ASN Q 103 GLN Q 275 GLN Q 310 HIS R 96 ASN R 103 GLN R 275 GLN R 310 HIS S 96 ASN S 103 GLN S 275 GLN S 310 HIS T 96 ASN T 103 GLN T 275 GLN T 310 HIS U 96 ASN U 103 GLN U 275 GLN U 310 HIS V 96 ASN V 103 GLN V 275 GLN V 310 HIS W 96 ASN W 103 GLN W 275 GLN W 310 HIS X 96 ASN X 103 GLN X 275 GLN X 310 HIS Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 61872 Z= 0.271 Angle : 0.635 6.363 83952 Z= 0.346 Chirality : 0.047 0.156 8808 Planarity : 0.005 0.033 10824 Dihedral : 6.697 71.932 8112 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.07 % Allowed : 9.72 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 7392 helix: 0.26 (0.10), residues: 2880 sheet: 0.56 (0.13), residues: 1776 loop : -0.87 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 80 HIS 0.005 0.001 HIS A 166 PHE 0.021 0.002 PHE A 163 TYR 0.012 0.002 TYR A 179 ARG 0.003 0.000 ARG K 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1272 time to evaluate : 5.341 Fit side-chains REVERT: A 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: B 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 170 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: D 170 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: E 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: F 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: G 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: H 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: I 170 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: J 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: K 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: L 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: M 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: N 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: O 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: P 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: Q 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: R 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: S 170 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: T 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: U 170 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: V 170 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: W 170 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: X 170 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7183 (mp0) outliers start: 262 outliers final: 47 residues processed: 1391 average time/residue: 1.6301 time to fit residues: 2846.3513 Evaluate side-chains 1316 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1245 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 668 optimal weight: 0.7980 chunk 508 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 454 optimal weight: 8.9990 chunk 679 optimal weight: 10.0000 chunk 719 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 643 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 103 GLN A 310 HIS B 96 ASN B 103 GLN B 310 HIS C 96 ASN C 103 GLN C 310 HIS D 96 ASN D 103 GLN D 310 HIS E 96 ASN E 103 GLN E 310 HIS F 96 ASN F 103 GLN F 310 HIS G 96 ASN G 103 GLN G 310 HIS H 96 ASN H 103 GLN H 310 HIS I 96 ASN I 103 GLN I 310 HIS J 96 ASN J 103 GLN J 310 HIS K 96 ASN K 103 GLN K 310 HIS L 96 ASN L 103 GLN L 310 HIS M 96 ASN M 103 GLN M 310 HIS N 96 ASN N 103 GLN N 310 HIS O 96 ASN O 103 GLN O 310 HIS P 96 ASN P 103 GLN P 310 HIS Q 96 ASN Q 103 GLN Q 310 HIS R 96 ASN R 103 GLN R 310 HIS S 96 ASN S 103 GLN S 310 HIS T 96 ASN T 103 GLN T 310 HIS U 96 ASN U 103 GLN U 310 HIS V 96 ASN V 103 GLN V 310 HIS W 96 ASN W 103 GLN W 310 HIS X 96 ASN X 103 GLN X 310 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 61872 Z= 0.247 Angle : 0.626 6.290 83952 Z= 0.337 Chirality : 0.047 0.154 8808 Planarity : 0.004 0.032 10824 Dihedral : 6.687 72.429 8112 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.36 % Allowed : 11.94 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 7392 helix: 0.55 (0.10), residues: 2880 sheet: 0.59 (0.13), residues: 1776 loop : -0.82 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 80 HIS 0.005 0.001 HIS E 166 PHE 0.020 0.002 PHE A 163 TYR 0.011 0.002 TYR A 179 ARG 0.002 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1269 time to evaluate : 5.314 Fit side-chains REVERT: A 170 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 170 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: C 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: E 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: F 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: G 170 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: H 170 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: I 170 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: J 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: K 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: L 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: M 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: N 170 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: O 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: P 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: Q 170 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: R 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: S 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: T 170 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: U 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: V 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: W 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: X 170 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7194 (mp0) outliers start: 216 outliers final: 71 residues processed: 1366 average time/residue: 1.5441 time to fit residues: 2673.4150 Evaluate side-chains 1293 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1198 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 598 optimal weight: 0.9990 chunk 408 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 535 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 613 optimal weight: 0.9990 chunk 497 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 367 optimal weight: 8.9990 chunk 645 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS B 310 HIS C 310 HIS D 310 HIS E 310 HIS F 310 HIS G 310 HIS H 310 HIS I 310 HIS J 310 HIS K 310 HIS L 310 HIS M 310 HIS N 310 HIS O 310 HIS P 310 HIS Q 310 HIS R 310 HIS S 310 HIS T 310 HIS U 310 HIS V 310 HIS W 310 HIS X 310 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 61872 Z= 0.139 Angle : 0.544 5.462 83952 Z= 0.284 Chirality : 0.044 0.135 8808 Planarity : 0.004 0.032 10824 Dihedral : 6.312 73.115 8112 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.21 % Allowed : 13.82 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 7392 helix: 0.90 (0.10), residues: 2880 sheet: 0.96 (0.13), residues: 1680 loop : -0.67 (0.12), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 302 HIS 0.004 0.001 HIS J 251 PHE 0.011 0.002 PHE A 163 TYR 0.010 0.001 TYR K 248 ARG 0.001 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1247 time to evaluate : 5.455 Fit side-chains REVERT: A 91 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7965 (tttt) REVERT: B 91 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (tttt) REVERT: C 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: D 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: E 91 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: F 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: G 91 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: H 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: I 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: J 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7955 (tttt) REVERT: K 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: L 91 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: M 91 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: N 91 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: O 91 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: P 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: Q 91 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (tttt) REVERT: R 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: S 91 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: T 91 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7953 (tttt) REVERT: U 91 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: V 91 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: W 91 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7950 (tttt) REVERT: X 91 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7954 (tttt) outliers start: 142 outliers final: 47 residues processed: 1294 average time/residue: 1.6068 time to fit residues: 2625.9554 Evaluate side-chains 1268 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1197 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 91 LYS Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 91 LYS Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 91 LYS Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 91 LYS Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 91 LYS Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 241 optimal weight: 1.9990 chunk 647 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 422 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 719 optimal weight: 10.0000 chunk 597 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 377 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 310 HIS B 310 HIS C 310 HIS D 310 HIS E 310 HIS F 310 HIS G 310 HIS H 310 HIS I 310 HIS J 103 GLN J 310 HIS K 225 ASN K 310 HIS L 310 HIS M 310 HIS N 310 HIS O 310 HIS P 310 HIS Q 310 HIS R 310 HIS S 310 HIS T 310 HIS U 310 HIS V 310 HIS W 310 HIS X 310 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 61872 Z= 0.271 Angle : 0.653 6.296 83952 Z= 0.348 Chirality : 0.048 0.154 8808 Planarity : 0.004 0.033 10824 Dihedral : 6.660 72.919 8112 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.60 % Allowed : 12.69 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 7392 helix: 0.77 (0.10), residues: 2880 sheet: 0.63 (0.13), residues: 1776 loop : -0.79 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 80 HIS 0.004 0.001 HIS A 166 PHE 0.021 0.002 PHE H 163 TYR 0.012 0.002 TYR R 179 ARG 0.003 0.000 ARG X 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1199 time to evaluate : 5.409 Fit side-chains REVERT: A 91 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: A 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 91 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7944 (tttt) REVERT: B 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: C 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: C 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: D 91 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: D 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: E 91 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7948 (tttt) REVERT: E 170 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: F 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: F 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: G 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: G 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: H 91 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: H 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: I 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: I 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: J 91 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: J 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: K 91 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: K 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: L 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: L 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: M 91 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: M 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: N 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: N 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: O 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: O 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: P 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: P 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: Q 91 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7944 (tttt) REVERT: Q 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: R 91 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: R 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: S 91 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: S 170 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: T 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: T 170 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: U 91 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7944 (tttt) REVERT: U 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: V 91 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: V 170 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: W 91 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: W 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: X 91 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: X 170 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7190 (mp0) outliers start: 167 outliers final: 71 residues processed: 1298 average time/residue: 1.5270 time to fit residues: 2515.3886 Evaluate side-chains 1319 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1200 time to evaluate : 5.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 215 LYS Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 215 LYS Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 91 LYS Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 91 LYS Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 91 LYS Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 215 LYS Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 91 LYS Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 215 LYS Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 215 LYS Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 215 LYS Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 215 LYS Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 91 LYS Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 215 LYS Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 91 LYS Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 215 LYS Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 694 optimal weight: 9.9990 chunk 81 optimal weight: 0.0370 chunk 410 optimal weight: 5.9990 chunk 525 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 605 optimal weight: 0.9990 chunk 401 optimal weight: 7.9990 chunk 717 optimal weight: 8.9990 chunk 448 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 310 HIS B 96 ASN B 310 HIS C 96 ASN C 310 HIS D 96 ASN D 310 HIS E 96 ASN E 310 HIS F 96 ASN F 310 HIS G 96 ASN G 310 HIS H 96 ASN H 310 HIS I 96 ASN I 310 HIS J 96 ASN J 310 HIS K 96 ASN K 310 HIS L 96 ASN L 310 HIS M 96 ASN M 310 HIS N 96 ASN N 310 HIS O 96 ASN O 310 HIS P 96 ASN P 310 HIS Q 96 ASN Q 310 HIS R 96 ASN R 310 HIS S 96 ASN S 310 HIS T 96 ASN T 310 HIS U 96 ASN U 310 HIS V 96 ASN V 310 HIS W 96 ASN W 310 HIS X 96 ASN X 310 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 61872 Z= 0.284 Angle : 0.657 6.410 83952 Z= 0.353 Chirality : 0.048 0.158 8808 Planarity : 0.005 0.032 10824 Dihedral : 6.741 72.907 8112 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 12.30 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 7392 helix: 0.71 (0.10), residues: 2880 sheet: 0.61 (0.13), residues: 1776 loop : -0.82 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 80 HIS 0.005 0.001 HIS R 166 PHE 0.022 0.002 PHE L 163 TYR 0.011 0.002 TYR A 179 ARG 0.003 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1210 time to evaluate : 5.362 Fit side-chains REVERT: A 170 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 170 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 170 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: D 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: E 170 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: F 170 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: G 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: H 170 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: I 170 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: J 170 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: K 170 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: L 170 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: M 170 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: N 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: O 170 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: P 170 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: Q 170 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: R 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: S 170 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: T 170 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: U 170 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: V 170 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: W 170 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: X 170 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7189 (mp0) outliers start: 193 outliers final: 94 residues processed: 1309 average time/residue: 1.5007 time to fit residues: 2504.4851 Evaluate side-chains 1311 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1193 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 147 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 147 VAL Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 443 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 428 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 455 optimal weight: 9.9990 chunk 488 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 563 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 103 GLN A 310 HIS B 96 ASN B 103 GLN B 310 HIS C 96 ASN C 103 GLN C 310 HIS D 96 ASN D 103 GLN D 310 HIS E 96 ASN E 103 GLN E 310 HIS F 96 ASN F 103 GLN F 310 HIS G 96 ASN G 103 GLN G 310 HIS H 96 ASN H 103 GLN H 310 HIS I 96 ASN I 103 GLN I 310 HIS J 96 ASN J 103 GLN J 310 HIS K 96 ASN K 103 GLN K 310 HIS L 96 ASN L 103 GLN L 310 HIS M 96 ASN M 103 GLN M 310 HIS N 96 ASN N 103 GLN N 310 HIS O 96 ASN O 103 GLN O 310 HIS P 96 ASN P 103 GLN P 310 HIS Q 96 ASN Q 103 GLN Q 310 HIS R 96 ASN R 103 GLN R 310 HIS S 96 ASN S 103 GLN S 310 HIS T 96 ASN T 103 GLN T 310 HIS U 96 ASN U 103 GLN U 310 HIS V 96 ASN V 103 GLN V 310 HIS W 96 ASN W 103 GLN W 310 HIS X 96 ASN X 103 GLN X 310 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 61872 Z= 0.318 Angle : 0.685 6.562 83952 Z= 0.368 Chirality : 0.050 0.161 8808 Planarity : 0.005 0.032 10824 Dihedral : 6.824 73.389 8112 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 11.77 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.10), residues: 7392 helix: 0.61 (0.10), residues: 2880 sheet: 0.59 (0.12), residues: 1776 loop : -0.83 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 80 HIS 0.005 0.001 HIS V 166 PHE 0.023 0.003 PHE I 163 TYR 0.012 0.002 TYR N 179 ARG 0.004 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1210 time to evaluate : 5.548 Fit side-chains REVERT: A 170 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: C 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: D 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: E 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: F 170 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: G 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: H 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: I 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: J 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: K 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: L 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: M 170 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: N 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: O 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: P 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: Q 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: R 170 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: S 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: T 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: U 170 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: V 170 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: W 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: X 170 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7198 (mp0) outliers start: 224 outliers final: 94 residues processed: 1332 average time/residue: 1.4621 time to fit residues: 2501.1081 Evaluate side-chains 1282 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1164 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 147 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 147 VAL Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 652 optimal weight: 0.7980 chunk 686 optimal weight: 6.9990 chunk 626 optimal weight: 6.9990 chunk 668 optimal weight: 10.0000 chunk 402 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 524 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 603 optimal weight: 9.9990 chunk 632 optimal weight: 10.0000 chunk 665 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 103 GLN A 310 HIS B 96 ASN B 103 GLN B 310 HIS C 96 ASN C 103 GLN C 310 HIS D 96 ASN D 103 GLN D 310 HIS E 96 ASN E 103 GLN E 310 HIS F 96 ASN F 103 GLN F 310 HIS G 96 ASN G 103 GLN G 310 HIS H 96 ASN H 103 GLN H 310 HIS I 96 ASN I 103 GLN I 310 HIS J 96 ASN J 310 HIS K 96 ASN K 103 GLN K 310 HIS L 96 ASN L 103 GLN L 310 HIS M 96 ASN M 103 GLN M 310 HIS N 96 ASN N 103 GLN N 310 HIS O 96 ASN O 103 GLN O 310 HIS P 96 ASN P 103 GLN P 310 HIS Q 96 ASN Q 103 GLN Q 310 HIS R 96 ASN R 103 GLN R 310 HIS S 96 ASN S 103 GLN S 310 HIS T 96 ASN T 103 GLN T 310 HIS U 96 ASN U 103 GLN U 310 HIS V 96 ASN V 103 GLN V 310 HIS W 96 ASN W 103 GLN W 310 HIS X 96 ASN X 103 GLN X 310 HIS Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 61872 Z= 0.239 Angle : 0.637 6.284 83952 Z= 0.340 Chirality : 0.047 0.153 8808 Planarity : 0.004 0.031 10824 Dihedral : 6.712 73.723 8112 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.90 % Allowed : 12.87 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7392 helix: 0.78 (0.10), residues: 2904 sheet: 0.69 (0.13), residues: 1752 loop : -0.82 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 80 HIS 0.005 0.001 HIS A 251 PHE 0.020 0.002 PHE L 163 TYR 0.009 0.002 TYR L 179 ARG 0.003 0.000 ARG U 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1228 time to evaluate : 5.371 Fit side-chains REVERT: A 170 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 170 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: C 170 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: D 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: E 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: F 170 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: G 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: H 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: I 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: J 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: K 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: L 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: M 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: N 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: O 170 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: P 170 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: Q 170 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: R 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: S 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: T 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: U 170 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: V 170 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: W 170 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: X 170 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7183 (mp0) outliers start: 122 outliers final: 93 residues processed: 1269 average time/residue: 1.5133 time to fit residues: 2448.3920 Evaluate side-chains 1293 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1176 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 170 GLU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 170 GLU Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 170 GLU Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain T residue 170 GLU Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 147 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 170 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 147 VAL Chi-restraints excluded: chain X residue 170 GLU Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 438 optimal weight: 5.9990 chunk 706 optimal weight: 0.9980 chunk 431 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 741 optimal weight: 1.9990 chunk 682 optimal weight: 10.0000 chunk 590 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 455 optimal weight: 10.0000 chunk 361 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 310 HIS B 103 GLN B 310 HIS C 103 GLN C 310 HIS D 103 GLN D 310 HIS E 103 GLN E 310 HIS F 103 GLN F 310 HIS G 103 GLN G 310 HIS H 103 GLN H 310 HIS I 103 GLN I 310 HIS J 103 GLN J 310 HIS K 103 GLN K 310 HIS L 103 GLN L 310 HIS M 103 GLN M 310 HIS N 103 GLN N 310 HIS O 103 GLN O 310 HIS P 103 GLN P 310 HIS Q 103 GLN Q 310 HIS R 103 GLN R 310 HIS S 103 GLN S 310 HIS T 103 GLN T 310 HIS U 103 GLN U 310 HIS V 103 GLN V 310 HIS W 103 GLN W 310 HIS X 103 GLN X 310 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 61872 Z= 0.162 Angle : 0.592 6.844 83952 Z= 0.307 Chirality : 0.045 0.152 8808 Planarity : 0.004 0.031 10824 Dihedral : 6.457 73.504 8112 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 13.43 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7392 helix: 0.86 (0.10), residues: 2856 sheet: 0.83 (0.13), residues: 1728 loop : -0.60 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 302 HIS 0.004 0.001 HIS A 251 PHE 0.014 0.002 PHE A 163 TYR 0.009 0.001 TYR A 248 ARG 0.003 0.000 ARG K 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14784 Ramachandran restraints generated. 7392 Oldfield, 0 Emsley, 7392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1248 time to evaluate : 5.379 Fit side-chains outliers start: 93 outliers final: 71 residues processed: 1291 average time/residue: 1.5032 time to fit residues: 2473.1828 Evaluate side-chains 1226 residues out of total 6432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1155 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain F residue 104 CYS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain I residue 104 CYS Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 272 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain K residue 104 CYS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain O residue 104 CYS Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 272 GLU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain S residue 104 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 272 GLU Chi-restraints excluded: chain T residue 104 CYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain T residue 272 GLU Chi-restraints excluded: chain U residue 104 CYS Chi-restraints excluded: chain U residue 147 VAL Chi-restraints excluded: chain U residue 272 GLU Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 272 GLU Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain X residue 147 VAL Chi-restraints excluded: chain X residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 468 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 544 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 591 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 607 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 225 ASN A 310 HIS B 103 GLN B 225 ASN B 310 HIS C 103 GLN C 225 ASN C 310 HIS D 103 GLN D 225 ASN D 310 HIS E 103 GLN E 225 ASN E 310 HIS F 103 GLN F 225 ASN F 310 HIS G 103 GLN G 225 ASN G 310 HIS H 103 GLN H 225 ASN H 310 HIS I 103 GLN I 225 ASN I 310 HIS J 103 GLN J 225 ASN J 310 HIS K 103 GLN K 225 ASN K 310 HIS L 103 GLN L 225 ASN L 310 HIS M 103 GLN M 225 ASN M 310 HIS N 103 GLN N 225 ASN N 310 HIS O 103 GLN O 225 ASN O 310 HIS P 103 GLN P 225 ASN P 310 HIS Q 103 GLN Q 225 ASN Q 310 HIS R 103 GLN R 225 ASN R 310 HIS S 103 GLN S 225 ASN S 310 HIS T 103 GLN T 225 ASN T 310 HIS U 103 GLN U 225 ASN U 310 HIS V 103 GLN V 225 ASN V 310 HIS W 103 GLN W 225 ASN W 310 HIS X 103 GLN X 225 ASN X 310 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103624 restraints weight = 48601.290| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 0.90 r_work: 0.2977 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 61872 Z= 0.307 Angle : 0.691 7.575 83952 Z= 0.367 Chirality : 0.049 0.166 8808 Planarity : 0.005 0.032 10824 Dihedral : 6.758 72.948 8112 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.46 % Allowed : 13.43 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7392 helix: 0.79 (0.10), residues: 2904 sheet: 0.68 (0.13), residues: 1752 loop : -0.87 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 80 HIS 0.005 0.001 HIS D 251 PHE 0.023 0.003 PHE G 163 TYR 0.009 0.002 TYR O 179 ARG 0.004 0.001 ARG J 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34637.74 seconds wall clock time: 587 minutes 54.30 seconds (35274.30 seconds total)