Starting phenix.real_space_refine on Sat Mar 16 12:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcp_8398/03_2024/5tcp_8398_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 45984 2.51 5 N 12912 2.21 5 O 13824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 138": "OE1" <-> "OE2" Residue "1 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 138": "OE1" <-> "OE2" Residue "3 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 138": "OE1" <-> "OE2" Residue "5 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 138": "OE1" <-> "OE2" Residue "7 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 138": "OE1" <-> "OE2" Residue "9 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "I TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "K TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "M TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "O TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "Q TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "S TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "U TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "Y TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 138": "OE1" <-> "OE2" Residue "a GLU 138": "OE1" <-> "OE2" Residue "b TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 138": "OE1" <-> "OE2" Residue "d TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 138": "OE1" <-> "OE2" Residue "h TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 138": "OE1" <-> "OE2" Residue "j TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 138": "OE1" <-> "OE2" Residue "l TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72888 Number of models: 1 Model: "" Number of chains: 48 Chain: "0" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "1" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "2" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "3" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "4" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "5" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "6" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "7" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "8" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "9" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "A" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "B" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "C" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "E" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "H" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "I" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "K" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "L" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "M" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "N" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "O" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "P" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "Q" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "R" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "S" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "T" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "U" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "V" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "W" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "X" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "Y" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "Z" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "a" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "b" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "c" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "e" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "f" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "g" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "h" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "i" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "j" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "k" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "l" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Time building chain proxies: 27.57, per 1000 atoms: 0.38 Number of scatterers: 72888 At special positions: 0 Unit cell: (261.63, 261.63, 78.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 13824 8.00 N 12912 7.00 C 45984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 22.25 Conformation dependent library (CDL) restraints added in 10.6 seconds 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17280 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 120 sheets defined 45.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain '0' and resid 28 through 42 Processing helix chain '0' and resid 52 through 54 No H-bonds generated for 'chain '0' and resid 52 through 54' Processing helix chain '0' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR 0 66 " --> pdb=" O GLU 0 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 0 67 " --> pdb=" O PRO 0 63 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 89 Processing helix chain '0' and resid 97 through 118 Processing helix chain '0' and resid 136 through 140 Processing helix chain '0' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 0 165 " --> pdb=" O ALA 0 161 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP 0 166 " --> pdb=" O HIS 0 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 0 167 " --> pdb=" O GLN 0 163 " (cutoff:3.500A) Processing helix chain '1' and resid 172 through 177 Processing helix chain '1' and resid 180 through 182 No H-bonds generated for 'chain '1' and resid 180 through 182' Processing helix chain '1' and resid 200 through 214 Processing helix chain '1' and resid 225 through 240 Processing helix chain '1' and resid 268 through 283 Processing helix chain '1' and resid 295 through 310 Processing helix chain '1' and resid 332 through 351 Processing helix chain '2' and resid 28 through 42 Processing helix chain '2' and resid 52 through 54 No H-bonds generated for 'chain '2' and resid 52 through 54' Processing helix chain '2' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 2 66 " --> pdb=" O GLU 2 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 2 67 " --> pdb=" O PRO 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 89 Processing helix chain '2' and resid 97 through 118 Processing helix chain '2' and resid 136 through 140 Processing helix chain '2' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 2 165 " --> pdb=" O ALA 2 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 2 166 " --> pdb=" O HIS 2 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 2 167 " --> pdb=" O GLN 2 163 " (cutoff:3.500A) Processing helix chain '3' and resid 172 through 177 Processing helix chain '3' and resid 180 through 182 No H-bonds generated for 'chain '3' and resid 180 through 182' Processing helix chain '3' and resid 200 through 214 Processing helix chain '3' and resid 225 through 240 Processing helix chain '3' and resid 268 through 283 Processing helix chain '3' and resid 295 through 310 Processing helix chain '3' and resid 332 through 351 Processing helix chain '4' and resid 28 through 42 Processing helix chain '4' and resid 52 through 54 No H-bonds generated for 'chain '4' and resid 52 through 54' Processing helix chain '4' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 4 66 " --> pdb=" O GLU 4 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 4 67 " --> pdb=" O PRO 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 89 Processing helix chain '4' and resid 97 through 118 Processing helix chain '4' and resid 136 through 140 Processing helix chain '4' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER 4 165 " --> pdb=" O ALA 4 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 4 166 " --> pdb=" O HIS 4 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 4 167 " --> pdb=" O GLN 4 163 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 177 Processing helix chain '5' and resid 180 through 182 No H-bonds generated for 'chain '5' and resid 180 through 182' Processing helix chain '5' and resid 200 through 214 Processing helix chain '5' and resid 225 through 240 Processing helix chain '5' and resid 268 through 283 Processing helix chain '5' and resid 295 through 310 Processing helix chain '5' and resid 332 through 351 Processing helix chain '6' and resid 28 through 42 Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR 6 66 " --> pdb=" O GLU 6 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA 6 67 " --> pdb=" O PRO 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 84 through 89 Processing helix chain '6' and resid 97 through 118 Processing helix chain '6' and resid 136 through 140 Processing helix chain '6' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 6 165 " --> pdb=" O ALA 6 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 6 166 " --> pdb=" O HIS 6 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 6 167 " --> pdb=" O GLN 6 163 " (cutoff:3.500A) Processing helix chain '7' and resid 172 through 177 Processing helix chain '7' and resid 180 through 182 No H-bonds generated for 'chain '7' and resid 180 through 182' Processing helix chain '7' and resid 200 through 214 Processing helix chain '7' and resid 225 through 240 Processing helix chain '7' and resid 268 through 283 Processing helix chain '7' and resid 295 through 310 Processing helix chain '7' and resid 332 through 351 Processing helix chain '8' and resid 28 through 42 Processing helix chain '8' and resid 52 through 54 No H-bonds generated for 'chain '8' and resid 52 through 54' Processing helix chain '8' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR 8 66 " --> pdb=" O GLU 8 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 8 67 " --> pdb=" O PRO 8 63 " (cutoff:3.500A) Processing helix chain '8' and resid 84 through 89 Processing helix chain '8' and resid 97 through 118 Processing helix chain '8' and resid 136 through 140 Processing helix chain '8' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER 8 165 " --> pdb=" O ALA 8 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP 8 166 " --> pdb=" O HIS 8 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 8 167 " --> pdb=" O GLN 8 163 " (cutoff:3.500A) Processing helix chain '9' and resid 172 through 177 Processing helix chain '9' and resid 180 through 182 No H-bonds generated for 'chain '9' and resid 180 through 182' Processing helix chain '9' and resid 200 through 214 Processing helix chain '9' and resid 225 through 240 Processing helix chain '9' and resid 268 through 283 Processing helix chain '9' and resid 295 through 310 Processing helix chain '9' and resid 332 through 351 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 97 through 118 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 200 through 214 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 268 through 283 Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 332 through 351 Processing helix chain 'D' and resid 28 through 42 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 97 through 118 Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP D 166 " --> pdb=" O HIS D 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 225 through 240 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 295 through 310 Processing helix chain 'E' and resid 332 through 351 Processing helix chain 'F' and resid 28 through 42 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA F 67 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 97 through 118 Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP F 166 " --> pdb=" O HIS F 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 200 through 214 Processing helix chain 'G' and resid 225 through 240 Processing helix chain 'G' and resid 268 through 283 Processing helix chain 'G' and resid 295 through 310 Processing helix chain 'G' and resid 332 through 351 Processing helix chain 'H' and resid 28 through 42 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA H 67 " --> pdb=" O PRO H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 97 through 118 Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP H 166 " --> pdb=" O HIS H 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 200 through 214 Processing helix chain 'I' and resid 225 through 240 Processing helix chain 'I' and resid 268 through 283 Processing helix chain 'I' and resid 295 through 310 Processing helix chain 'I' and resid 332 through 351 Processing helix chain 'J' and resid 28 through 42 Processing helix chain 'J' and resid 52 through 54 No H-bonds generated for 'chain 'J' and resid 52 through 54' Processing helix chain 'J' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA J 67 " --> pdb=" O PRO J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 97 through 118 Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP J 166 " --> pdb=" O HIS J 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE J 167 " --> pdb=" O GLN J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 Processing helix chain 'K' and resid 180 through 182 No H-bonds generated for 'chain 'K' and resid 180 through 182' Processing helix chain 'K' and resid 200 through 214 Processing helix chain 'K' and resid 225 through 240 Processing helix chain 'K' and resid 268 through 283 Processing helix chain 'K' and resid 295 through 310 Processing helix chain 'K' and resid 332 through 351 Processing helix chain 'L' and resid 28 through 42 Processing helix chain 'L' and resid 52 through 54 No H-bonds generated for 'chain 'L' and resid 52 through 54' Processing helix chain 'L' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA L 67 " --> pdb=" O PRO L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 97 through 118 Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP L 166 " --> pdb=" O HIS L 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE L 167 " --> pdb=" O GLN L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 177 Processing helix chain 'M' and resid 180 through 182 No H-bonds generated for 'chain 'M' and resid 180 through 182' Processing helix chain 'M' and resid 200 through 214 Processing helix chain 'M' and resid 225 through 240 Processing helix chain 'M' and resid 268 through 283 Processing helix chain 'M' and resid 295 through 310 Processing helix chain 'M' and resid 332 through 351 Processing helix chain 'N' and resid 28 through 42 Processing helix chain 'N' and resid 52 through 54 No H-bonds generated for 'chain 'N' and resid 52 through 54' Processing helix chain 'N' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA N 67 " --> pdb=" O PRO N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 89 Processing helix chain 'N' and resid 97 through 118 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER N 165 " --> pdb=" O ALA N 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP N 166 " --> pdb=" O HIS N 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE N 167 " --> pdb=" O GLN N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 177 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 200 through 214 Processing helix chain 'O' and resid 225 through 240 Processing helix chain 'O' and resid 268 through 283 Processing helix chain 'O' and resid 295 through 310 Processing helix chain 'O' and resid 332 through 351 Processing helix chain 'P' and resid 28 through 42 Processing helix chain 'P' and resid 52 through 54 No H-bonds generated for 'chain 'P' and resid 52 through 54' Processing helix chain 'P' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR P 66 " --> pdb=" O GLU P 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 89 Processing helix chain 'P' and resid 97 through 118 Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER P 165 " --> pdb=" O ALA P 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP P 166 " --> pdb=" O HIS P 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE P 167 " --> pdb=" O GLN P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 177 Processing helix chain 'Q' and resid 180 through 182 No H-bonds generated for 'chain 'Q' and resid 180 through 182' Processing helix chain 'Q' and resid 200 through 214 Processing helix chain 'Q' and resid 225 through 240 Processing helix chain 'Q' and resid 268 through 283 Processing helix chain 'Q' and resid 295 through 310 Processing helix chain 'Q' and resid 332 through 351 Processing helix chain 'R' and resid 28 through 42 Processing helix chain 'R' and resid 52 through 54 No H-bonds generated for 'chain 'R' and resid 52 through 54' Processing helix chain 'R' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR R 66 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA R 67 " --> pdb=" O PRO R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 97 through 118 Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 177 Processing helix chain 'S' and resid 180 through 182 No H-bonds generated for 'chain 'S' and resid 180 through 182' Processing helix chain 'S' and resid 200 through 214 Processing helix chain 'S' and resid 225 through 240 Processing helix chain 'S' and resid 268 through 283 Processing helix chain 'S' and resid 295 through 310 Processing helix chain 'S' and resid 332 through 351 Processing helix chain 'T' and resid 28 through 42 Processing helix chain 'T' and resid 52 through 54 No H-bonds generated for 'chain 'T' and resid 52 through 54' Processing helix chain 'T' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR T 66 " --> pdb=" O GLU T 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA T 67 " --> pdb=" O PRO T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 89 Processing helix chain 'T' and resid 97 through 118 Processing helix chain 'T' and resid 136 through 140 Processing helix chain 'T' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER T 165 " --> pdb=" O ALA T 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP T 166 " --> pdb=" O HIS T 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE T 167 " --> pdb=" O GLN T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 177 Processing helix chain 'U' and resid 180 through 182 No H-bonds generated for 'chain 'U' and resid 180 through 182' Processing helix chain 'U' and resid 200 through 214 Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 268 through 283 Processing helix chain 'U' and resid 295 through 310 Processing helix chain 'U' and resid 332 through 351 Processing helix chain 'V' and resid 28 through 42 Processing helix chain 'V' and resid 52 through 54 No H-bonds generated for 'chain 'V' and resid 52 through 54' Processing helix chain 'V' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR V 66 " --> pdb=" O GLU V 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA V 67 " --> pdb=" O PRO V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 89 Processing helix chain 'V' and resid 97 through 118 Processing helix chain 'V' and resid 136 through 140 Processing helix chain 'V' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP V 166 " --> pdb=" O HIS V 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE V 167 " --> pdb=" O GLN V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 177 Processing helix chain 'W' and resid 180 through 182 No H-bonds generated for 'chain 'W' and resid 180 through 182' Processing helix chain 'W' and resid 200 through 214 Processing helix chain 'W' and resid 225 through 240 Processing helix chain 'W' and resid 268 through 283 Processing helix chain 'W' and resid 295 through 310 Processing helix chain 'W' and resid 332 through 351 Processing helix chain 'X' and resid 28 through 42 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR X 66 " --> pdb=" O GLU X 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA X 67 " --> pdb=" O PRO X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 89 Processing helix chain 'X' and resid 97 through 118 Processing helix chain 'X' and resid 136 through 140 Processing helix chain 'X' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER X 165 " --> pdb=" O ALA X 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP X 166 " --> pdb=" O HIS X 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE X 167 " --> pdb=" O GLN X 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 177 Processing helix chain 'Y' and resid 180 through 182 No H-bonds generated for 'chain 'Y' and resid 180 through 182' Processing helix chain 'Y' and resid 200 through 214 Processing helix chain 'Y' and resid 225 through 240 Processing helix chain 'Y' and resid 268 through 283 Processing helix chain 'Y' and resid 295 through 310 Processing helix chain 'Y' and resid 332 through 351 Processing helix chain 'Z' and resid 28 through 42 Processing helix chain 'Z' and resid 52 through 54 No H-bonds generated for 'chain 'Z' and resid 52 through 54' Processing helix chain 'Z' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA Z 67 " --> pdb=" O PRO Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 89 Processing helix chain 'Z' and resid 97 through 118 Processing helix chain 'Z' and resid 136 through 140 Processing helix chain 'Z' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER Z 165 " --> pdb=" O ALA Z 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP Z 166 " --> pdb=" O HIS Z 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 167 " --> pdb=" O GLN Z 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 42 Processing helix chain 'a' and resid 52 through 54 No H-bonds generated for 'chain 'a' and resid 52 through 54' Processing helix chain 'a' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR a 66 " --> pdb=" O GLU a 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA a 67 " --> pdb=" O PRO a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 Processing helix chain 'a' and resid 97 through 118 Processing helix chain 'a' and resid 136 through 140 Processing helix chain 'a' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER a 165 " --> pdb=" O ALA a 161 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP a 166 " --> pdb=" O HIS a 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE a 167 " --> pdb=" O GLN a 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 180 through 182 No H-bonds generated for 'chain 'b' and resid 180 through 182' Processing helix chain 'b' and resid 200 through 214 Processing helix chain 'b' and resid 225 through 240 Processing helix chain 'b' and resid 268 through 283 Processing helix chain 'b' and resid 295 through 310 Processing helix chain 'b' and resid 332 through 351 Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'c' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR c 66 " --> pdb=" O GLU c 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 89 Processing helix chain 'c' and resid 97 through 118 Processing helix chain 'c' and resid 136 through 140 Processing helix chain 'c' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER c 165 " --> pdb=" O ALA c 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE c 167 " --> pdb=" O GLN c 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 177 Processing helix chain 'd' and resid 180 through 182 No H-bonds generated for 'chain 'd' and resid 180 through 182' Processing helix chain 'd' and resid 200 through 214 Processing helix chain 'd' and resid 225 through 240 Processing helix chain 'd' and resid 268 through 283 Processing helix chain 'd' and resid 295 through 310 Processing helix chain 'd' and resid 332 through 351 Processing helix chain 'e' and resid 28 through 42 Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 61 through 75 removed outlier: 4.499A pdb=" N THR e 66 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA e 67 " --> pdb=" O PRO e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 97 through 118 Processing helix chain 'e' and resid 136 through 140 Processing helix chain 'e' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER e 165 " --> pdb=" O ALA e 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP e 166 " --> pdb=" O HIS e 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE e 167 " --> pdb=" O GLN e 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 177 Processing helix chain 'f' and resid 180 through 182 No H-bonds generated for 'chain 'f' and resid 180 through 182' Processing helix chain 'f' and resid 200 through 214 Processing helix chain 'f' and resid 225 through 240 Processing helix chain 'f' and resid 268 through 283 Processing helix chain 'f' and resid 295 through 310 Processing helix chain 'f' and resid 332 through 351 Processing helix chain 'g' and resid 28 through 42 Processing helix chain 'g' and resid 52 through 54 No H-bonds generated for 'chain 'g' and resid 52 through 54' Processing helix chain 'g' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA g 67 " --> pdb=" O PRO g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 89 Processing helix chain 'g' and resid 97 through 118 Processing helix chain 'g' and resid 136 through 140 Processing helix chain 'g' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER g 165 " --> pdb=" O ALA g 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP g 166 " --> pdb=" O HIS g 162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE g 167 " --> pdb=" O GLN g 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 177 Processing helix chain 'h' and resid 180 through 182 No H-bonds generated for 'chain 'h' and resid 180 through 182' Processing helix chain 'h' and resid 200 through 214 Processing helix chain 'h' and resid 225 through 240 Processing helix chain 'h' and resid 268 through 283 Processing helix chain 'h' and resid 295 through 310 Processing helix chain 'h' and resid 332 through 351 Processing helix chain 'i' and resid 28 through 42 Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR i 66 " --> pdb=" O GLU i 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA i 67 " --> pdb=" O PRO i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 89 Processing helix chain 'i' and resid 97 through 118 Processing helix chain 'i' and resid 136 through 140 Processing helix chain 'i' and resid 159 through 173 removed outlier: 5.433A pdb=" N SER i 165 " --> pdb=" O ALA i 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP i 166 " --> pdb=" O HIS i 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE i 167 " --> pdb=" O GLN i 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 172 through 177 Processing helix chain 'j' and resid 180 through 182 No H-bonds generated for 'chain 'j' and resid 180 through 182' Processing helix chain 'j' and resid 200 through 214 Processing helix chain 'j' and resid 225 through 240 Processing helix chain 'j' and resid 268 through 283 Processing helix chain 'j' and resid 295 through 310 Processing helix chain 'j' and resid 332 through 351 Processing helix chain 'k' and resid 28 through 42 Processing helix chain 'k' and resid 52 through 54 No H-bonds generated for 'chain 'k' and resid 52 through 54' Processing helix chain 'k' and resid 61 through 75 removed outlier: 4.500A pdb=" N THR k 66 " --> pdb=" O GLU k 62 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA k 67 " --> pdb=" O PRO k 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 89 Processing helix chain 'k' and resid 97 through 118 Processing helix chain 'k' and resid 136 through 140 Processing helix chain 'k' and resid 159 through 173 removed outlier: 5.434A pdb=" N SER k 165 " --> pdb=" O ALA k 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP k 166 " --> pdb=" O HIS k 162 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE k 167 " --> pdb=" O GLN k 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 172 through 177 Processing helix chain 'l' and resid 180 through 182 No H-bonds generated for 'chain 'l' and resid 180 through 182' Processing helix chain 'l' and resid 200 through 214 Processing helix chain 'l' and resid 225 through 240 Processing helix chain 'l' and resid 268 through 283 Processing helix chain 'l' and resid 295 through 310 Processing helix chain 'l' and resid 332 through 351 Processing sheet with id=AA1, first strand: chain '0' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 0 58 " --> pdb=" O LEU 0 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 0 25 " --> pdb=" O TYR 0 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 0 56 " --> pdb=" O LYS 0 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL 0 153 " --> pdb=" O LEU 0 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 0 126 " --> pdb=" O LEU 0 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 0 151 " --> pdb=" O ALA 0 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 0 128 " --> pdb=" O SER 0 149 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER 0 149 " --> pdb=" O VAL 0 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 0 148 " --> pdb=" O SER 0 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 0 186 " --> pdb=" O LEU 0 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 0 150 " --> pdb=" O VAL 0 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER 0 188 " --> pdb=" O ALA 0 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 0 152 " --> pdb=" O SER 0 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 1 194 " --> pdb=" O ARG 1 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 1 223 " --> pdb=" O LEU 1 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 1 196 " --> pdb=" O ILE 1 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 1 245 " --> pdb=" O SER 1 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 1 261 " --> pdb=" O TYR 1 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 1 247 " --> pdb=" O TRP 1 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 1 258 " --> pdb=" O THR 1 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 1 294 " --> pdb=" O PHE 1 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 1 260 " --> pdb=" O MET 1 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL 1 323 " --> pdb=" O GLN 1 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 1 358 " --> pdb=" O VAL 1 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 1 325 " --> pdb=" O ALA 1 358 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU 1 360 " --> pdb=" O PHE 1 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 1 327 " --> pdb=" O GLU 1 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 2 58 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 2 25 " --> pdb=" O TYR 2 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 2 56 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 2 153 " --> pdb=" O LEU 2 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA 2 126 " --> pdb=" O LEU 2 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 2 151 " --> pdb=" O ALA 2 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL 2 128 " --> pdb=" O SER 2 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 2 149 " --> pdb=" O VAL 2 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 2 148 " --> pdb=" O SER 2 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL 2 186 " --> pdb=" O LEU 2 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 2 150 " --> pdb=" O VAL 2 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER 2 188 " --> pdb=" O ALA 2 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 2 152 " --> pdb=" O SER 2 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 3 194 " --> pdb=" O ARG 3 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 3 223 " --> pdb=" O LEU 3 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 3 245 " --> pdb=" O SER 3 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER 3 261 " --> pdb=" O TYR 3 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 3 247 " --> pdb=" O TRP 3 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 3 258 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 3 294 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 3 260 " --> pdb=" O MET 3 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL 3 323 " --> pdb=" O GLN 3 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 3 358 " --> pdb=" O VAL 3 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 3 325 " --> pdb=" O ALA 3 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU 3 360 " --> pdb=" O PHE 3 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 3 327 " --> pdb=" O GLU 3 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 4 58 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS 4 25 " --> pdb=" O TYR 4 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR 4 56 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 4 153 " --> pdb=" O LEU 4 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 4 126 " --> pdb=" O LEU 4 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 4 151 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 4 128 " --> pdb=" O SER 4 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 4 149 " --> pdb=" O VAL 4 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 4 148 " --> pdb=" O SER 4 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 4 186 " --> pdb=" O LEU 4 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA 4 150 " --> pdb=" O VAL 4 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 4 188 " --> pdb=" O ALA 4 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 4 152 " --> pdb=" O SER 4 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 5 194 " --> pdb=" O ARG 5 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE 5 223 " --> pdb=" O LEU 5 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 5 196 " --> pdb=" O ILE 5 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 5 245 " --> pdb=" O SER 5 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 5 261 " --> pdb=" O TYR 5 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 5 247 " --> pdb=" O TRP 5 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE 5 258 " --> pdb=" O THR 5 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 5 294 " --> pdb=" O PHE 5 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU 5 260 " --> pdb=" O MET 5 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL 5 323 " --> pdb=" O GLN 5 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA 5 358 " --> pdb=" O VAL 5 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 5 325 " --> pdb=" O ALA 5 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU 5 360 " --> pdb=" O PHE 5 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 5 327 " --> pdb=" O GLU 5 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 6 58 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 6 25 " --> pdb=" O TYR 6 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 6 56 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 6 153 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 6 126 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 6 151 " --> pdb=" O ALA 6 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL 6 128 " --> pdb=" O SER 6 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 6 149 " --> pdb=" O VAL 6 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU 6 148 " --> pdb=" O SER 6 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 6 186 " --> pdb=" O LEU 6 148 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA 6 150 " --> pdb=" O VAL 6 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 6 188 " --> pdb=" O ALA 6 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 6 152 " --> pdb=" O SER 6 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU 7 194 " --> pdb=" O ARG 7 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 7 223 " --> pdb=" O LEU 7 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 7 196 " --> pdb=" O ILE 7 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '7' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR 7 245 " --> pdb=" O SER 7 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER 7 261 " --> pdb=" O TYR 7 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 7 247 " --> pdb=" O TRP 7 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE 7 258 " --> pdb=" O THR 7 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET 7 294 " --> pdb=" O PHE 7 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 7 260 " --> pdb=" O MET 7 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL 7 323 " --> pdb=" O GLN 7 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA 7 358 " --> pdb=" O VAL 7 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 7 325 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU 7 360 " --> pdb=" O PHE 7 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 7 327 " --> pdb=" O GLU 7 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '8' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE 8 58 " --> pdb=" O LEU 8 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS 8 25 " --> pdb=" O TYR 8 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR 8 56 " --> pdb=" O LYS 8 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '8' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL 8 153 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA 8 126 " --> pdb=" O LEU 8 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 8 151 " --> pdb=" O ALA 8 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 8 128 " --> pdb=" O SER 8 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 8 149 " --> pdb=" O VAL 8 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU 8 148 " --> pdb=" O SER 8 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL 8 186 " --> pdb=" O LEU 8 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA 8 150 " --> pdb=" O VAL 8 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER 8 188 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA 8 152 " --> pdb=" O SER 8 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '9' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU 9 194 " --> pdb=" O ARG 9 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE 9 223 " --> pdb=" O LEU 9 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL 9 196 " --> pdb=" O ILE 9 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '9' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR 9 245 " --> pdb=" O SER 9 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER 9 261 " --> pdb=" O TYR 9 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG 9 247 " --> pdb=" O TRP 9 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE 9 258 " --> pdb=" O THR 9 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET 9 294 " --> pdb=" O PHE 9 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 9 260 " --> pdb=" O MET 9 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '9' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL 9 323 " --> pdb=" O GLN 9 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA 9 358 " --> pdb=" O VAL 9 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE 9 325 " --> pdb=" O ALA 9 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU 9 360 " --> pdb=" O PHE 9 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE 9 327 " --> pdb=" O GLU 9 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU A 194 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE A 223 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 196 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR A 245 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER A 261 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 247 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 258 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 294 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 260 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL A 323 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 358 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 325 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU A 360 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 327 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE B 58 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 25 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 56 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL B 153 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 126 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 151 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL B 128 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER B 149 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 148 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL B 186 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA B 150 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER B 188 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 152 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU C 194 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE C 223 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 196 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR C 245 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 261 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG C 247 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE C 258 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET C 294 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU C 260 " --> pdb=" O MET C 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL C 323 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA C 358 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE C 325 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU C 360 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 327 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE D 58 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS D 25 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR D 56 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL D 153 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 126 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 151 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 128 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER D 149 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 148 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL D 186 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA D 150 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER D 188 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA D 152 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU E 194 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE E 223 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 196 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR E 245 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER E 261 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG E 247 " --> pdb=" O TRP E 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE E 258 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET E 294 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 260 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL E 323 " --> pdb=" O GLN E 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA E 358 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE E 325 " --> pdb=" O ALA E 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU E 360 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE E 327 " --> pdb=" O GLU E 360 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE F 58 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS F 25 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR F 56 " --> pdb=" O LYS F 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL F 153 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA F 126 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 151 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 128 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER F 149 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU F 148 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL F 186 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA F 150 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER F 188 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA F 152 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU G 194 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE G 223 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL G 196 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR G 245 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG G 247 " --> pdb=" O TRP G 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE G 258 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET G 294 " --> pdb=" O PHE G 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU G 260 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL G 323 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA G 358 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE G 325 " --> pdb=" O ALA G 358 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU G 360 " --> pdb=" O PHE G 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE G 327 " --> pdb=" O GLU G 360 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE H 58 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS H 25 " --> pdb=" O TYR H 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR H 56 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL H 153 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA H 126 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 151 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL H 128 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER H 149 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU H 148 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL H 186 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA H 150 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER H 188 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA H 152 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU I 194 " --> pdb=" O ARG I 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE I 223 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL I 196 " --> pdb=" O ILE I 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR I 245 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER I 261 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG I 247 " --> pdb=" O TRP I 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE I 258 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET I 294 " --> pdb=" O PHE I 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU I 260 " --> pdb=" O MET I 294 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL I 323 " --> pdb=" O GLN I 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA I 358 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE I 325 " --> pdb=" O ALA I 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU I 360 " --> pdb=" O PHE I 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE I 327 " --> pdb=" O GLU I 360 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE J 58 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS J 25 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR J 56 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL J 153 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA J 126 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU J 151 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL J 128 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER J 149 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU J 148 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL J 186 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA J 150 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER J 188 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA J 152 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU K 194 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE K 223 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL K 196 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR K 245 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER K 261 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG K 247 " --> pdb=" O TRP K 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE K 258 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET K 294 " --> pdb=" O PHE K 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 260 " --> pdb=" O MET K 294 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL K 323 " --> pdb=" O GLN K 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA K 358 " --> pdb=" O VAL K 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE K 325 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU K 360 " --> pdb=" O PHE K 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE K 327 " --> pdb=" O GLU K 360 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE L 58 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS L 25 " --> pdb=" O TYR L 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR L 56 " --> pdb=" O LYS L 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL L 153 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA L 126 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU L 151 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL L 128 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER L 149 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 148 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL L 186 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA L 150 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER L 188 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA L 152 " --> pdb=" O SER L 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU M 194 " --> pdb=" O ARG M 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE M 223 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL M 196 " --> pdb=" O ILE M 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR M 245 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER M 261 " --> pdb=" O TYR M 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG M 247 " --> pdb=" O TRP M 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE M 258 " --> pdb=" O THR M 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET M 294 " --> pdb=" O PHE M 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU M 260 " --> pdb=" O MET M 294 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL M 323 " --> pdb=" O GLN M 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA M 358 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE M 325 " --> pdb=" O ALA M 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU M 360 " --> pdb=" O PHE M 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE M 327 " --> pdb=" O GLU M 360 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE N 58 " --> pdb=" O LEU N 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS N 25 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR N 56 " --> pdb=" O LYS N 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL N 153 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA N 126 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU N 151 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL N 128 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER N 149 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU N 148 " --> pdb=" O SER N 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL N 186 " --> pdb=" O LEU N 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA N 150 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER N 188 " --> pdb=" O ALA N 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA N 152 " --> pdb=" O SER N 188 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU O 194 " --> pdb=" O ARG O 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE O 223 " --> pdb=" O LEU O 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 196 " --> pdb=" O ILE O 223 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR O 245 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER O 261 " --> pdb=" O TYR O 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG O 247 " --> pdb=" O TRP O 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE O 258 " --> pdb=" O THR O 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET O 294 " --> pdb=" O PHE O 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU O 260 " --> pdb=" O MET O 294 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL O 323 " --> pdb=" O GLN O 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA O 358 " --> pdb=" O VAL O 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE O 325 " --> pdb=" O ALA O 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU O 360 " --> pdb=" O PHE O 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE O 327 " --> pdb=" O GLU O 360 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE P 58 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS P 25 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR P 56 " --> pdb=" O LYS P 25 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL P 153 " --> pdb=" O LEU P 124 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA P 126 " --> pdb=" O LEU P 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU P 151 " --> pdb=" O ALA P 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL P 128 " --> pdb=" O SER P 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER P 149 " --> pdb=" O VAL P 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU P 148 " --> pdb=" O SER P 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL P 186 " --> pdb=" O LEU P 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA P 150 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER P 188 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA P 152 " --> pdb=" O SER P 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU Q 194 " --> pdb=" O ARG Q 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE Q 223 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL Q 196 " --> pdb=" O ILE Q 223 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR Q 245 " --> pdb=" O SER Q 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER Q 261 " --> pdb=" O TYR Q 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG Q 247 " --> pdb=" O TRP Q 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE Q 258 " --> pdb=" O THR Q 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET Q 294 " --> pdb=" O PHE Q 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU Q 260 " --> pdb=" O MET Q 294 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL Q 323 " --> pdb=" O GLN Q 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA Q 358 " --> pdb=" O VAL Q 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE Q 325 " --> pdb=" O ALA Q 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU Q 360 " --> pdb=" O PHE Q 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE Q 327 " --> pdb=" O GLU Q 360 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE R 58 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS R 25 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR R 56 " --> pdb=" O LYS R 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL R 153 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA R 126 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU R 151 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL R 128 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER R 149 " --> pdb=" O VAL R 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU R 148 " --> pdb=" O SER R 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL R 186 " --> pdb=" O LEU R 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA R 150 " --> pdb=" O VAL R 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER R 188 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA R 152 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU S 194 " --> pdb=" O ARG S 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE S 223 " --> pdb=" O LEU S 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL S 196 " --> pdb=" O ILE S 223 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'S' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR S 245 " --> pdb=" O SER S 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER S 261 " --> pdb=" O TYR S 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG S 247 " --> pdb=" O TRP S 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE S 258 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET S 294 " --> pdb=" O PHE S 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU S 260 " --> pdb=" O MET S 294 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL S 323 " --> pdb=" O GLN S 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA S 358 " --> pdb=" O VAL S 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE S 325 " --> pdb=" O ALA S 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU S 360 " --> pdb=" O PHE S 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE S 327 " --> pdb=" O GLU S 360 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE T 58 " --> pdb=" O LEU T 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS T 25 " --> pdb=" O TYR T 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR T 56 " --> pdb=" O LYS T 25 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL T 153 " --> pdb=" O LEU T 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA T 126 " --> pdb=" O LEU T 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU T 151 " --> pdb=" O ALA T 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL T 128 " --> pdb=" O SER T 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER T 149 " --> pdb=" O VAL T 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU T 148 " --> pdb=" O SER T 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL T 186 " --> pdb=" O LEU T 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA T 150 " --> pdb=" O VAL T 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER T 188 " --> pdb=" O ALA T 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA T 152 " --> pdb=" O SER T 188 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU U 194 " --> pdb=" O ARG U 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE U 223 " --> pdb=" O LEU U 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL U 196 " --> pdb=" O ILE U 223 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR U 245 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER U 261 " --> pdb=" O TYR U 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG U 247 " --> pdb=" O TRP U 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE U 258 " --> pdb=" O THR U 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET U 294 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU U 260 " --> pdb=" O MET U 294 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL U 323 " --> pdb=" O GLN U 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA U 358 " --> pdb=" O VAL U 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE U 325 " --> pdb=" O ALA U 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU U 360 " --> pdb=" O PHE U 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE U 327 " --> pdb=" O GLU U 360 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE V 58 " --> pdb=" O LEU V 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS V 25 " --> pdb=" O TYR V 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR V 56 " --> pdb=" O LYS V 25 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'V' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL V 153 " --> pdb=" O LEU V 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA V 126 " --> pdb=" O LEU V 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU V 151 " --> pdb=" O ALA V 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL V 128 " --> pdb=" O SER V 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER V 149 " --> pdb=" O VAL V 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU V 148 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL V 186 " --> pdb=" O LEU V 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA V 150 " --> pdb=" O VAL V 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER V 188 " --> pdb=" O ALA V 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA V 152 " --> pdb=" O SER V 188 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU W 194 " --> pdb=" O ARG W 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE W 223 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL W 196 " --> pdb=" O ILE W 223 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR W 245 " --> pdb=" O SER W 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER W 261 " --> pdb=" O TYR W 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG W 247 " --> pdb=" O TRP W 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE W 258 " --> pdb=" O THR W 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET W 294 " --> pdb=" O PHE W 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU W 260 " --> pdb=" O MET W 294 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL W 323 " --> pdb=" O GLN W 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA W 358 " --> pdb=" O VAL W 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE W 325 " --> pdb=" O ALA W 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU W 360 " --> pdb=" O PHE W 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE W 327 " --> pdb=" O GLU W 360 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'X' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE X 58 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS X 25 " --> pdb=" O TYR X 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR X 56 " --> pdb=" O LYS X 25 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'X' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL X 153 " --> pdb=" O LEU X 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA X 126 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU X 151 " --> pdb=" O ALA X 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL X 128 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER X 149 " --> pdb=" O VAL X 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU X 148 " --> pdb=" O SER X 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL X 186 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA X 150 " --> pdb=" O VAL X 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER X 188 " --> pdb=" O ALA X 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA X 152 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Y' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU Y 194 " --> pdb=" O ARG Y 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE Y 223 " --> pdb=" O LEU Y 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL Y 196 " --> pdb=" O ILE Y 223 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 245 through 249 removed outlier: 6.522A pdb=" N TYR Y 245 " --> pdb=" O SER Y 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER Y 261 " --> pdb=" O TYR Y 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG Y 247 " --> pdb=" O TRP Y 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE Y 258 " --> pdb=" O THR Y 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET Y 294 " --> pdb=" O PHE Y 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU Y 260 " --> pdb=" O MET Y 294 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL Y 323 " --> pdb=" O GLN Y 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA Y 358 " --> pdb=" O VAL Y 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE Y 325 " --> pdb=" O ALA Y 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU Y 360 " --> pdb=" O PHE Y 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE Y 327 " --> pdb=" O GLU Y 360 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Z' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE Z 58 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS Z 25 " --> pdb=" O TYR Z 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR Z 56 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL Z 153 " --> pdb=" O LEU Z 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA Z 126 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU Z 151 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL Z 128 " --> pdb=" O SER Z 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER Z 149 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU Z 148 " --> pdb=" O SER Z 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL Z 186 " --> pdb=" O LEU Z 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA Z 150 " --> pdb=" O VAL Z 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER Z 188 " --> pdb=" O ALA Z 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA Z 152 " --> pdb=" O SER Z 188 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'a' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE a 58 " --> pdb=" O LEU a 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS a 25 " --> pdb=" O TYR a 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR a 56 " --> pdb=" O LYS a 25 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'a' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL a 153 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA a 126 " --> pdb=" O LEU a 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU a 151 " --> pdb=" O ALA a 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL a 128 " --> pdb=" O SER a 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER a 149 " --> pdb=" O VAL a 128 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU a 148 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL a 186 " --> pdb=" O LEU a 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA a 150 " --> pdb=" O VAL a 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER a 188 " --> pdb=" O ALA a 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA a 152 " --> pdb=" O SER a 188 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'b' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU b 194 " --> pdb=" O ARG b 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE b 223 " --> pdb=" O LEU b 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL b 196 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR b 245 " --> pdb=" O SER b 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER b 261 " --> pdb=" O TYR b 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG b 247 " --> pdb=" O TRP b 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE b 258 " --> pdb=" O THR b 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET b 294 " --> pdb=" O PHE b 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU b 260 " --> pdb=" O MET b 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL b 323 " --> pdb=" O GLN b 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA b 358 " --> pdb=" O VAL b 323 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE b 325 " --> pdb=" O ALA b 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU b 360 " --> pdb=" O PHE b 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE b 327 " --> pdb=" O GLU b 360 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'c' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE c 58 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS c 25 " --> pdb=" O TYR c 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR c 56 " --> pdb=" O LYS c 25 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'c' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL c 153 " --> pdb=" O LEU c 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA c 126 " --> pdb=" O LEU c 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU c 151 " --> pdb=" O ALA c 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL c 128 " --> pdb=" O SER c 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER c 149 " --> pdb=" O VAL c 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU c 148 " --> pdb=" O SER c 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL c 186 " --> pdb=" O LEU c 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA c 150 " --> pdb=" O VAL c 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER c 188 " --> pdb=" O ALA c 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA c 152 " --> pdb=" O SER c 188 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'd' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU d 194 " --> pdb=" O ARG d 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE d 223 " --> pdb=" O LEU d 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL d 196 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'd' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR d 245 " --> pdb=" O SER d 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER d 261 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG d 247 " --> pdb=" O TRP d 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE d 258 " --> pdb=" O THR d 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET d 294 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU d 260 " --> pdb=" O MET d 294 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'd' and resid 315 through 319 removed outlier: 6.522A pdb=" N VAL d 323 " --> pdb=" O GLN d 356 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA d 358 " --> pdb=" O VAL d 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE d 325 " --> pdb=" O ALA d 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU d 360 " --> pdb=" O PHE d 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE d 327 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'e' and resid 21 through 27 removed outlier: 6.550A pdb=" N ILE e 58 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS e 25 " --> pdb=" O TYR e 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR e 56 " --> pdb=" O LYS e 25 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'e' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL e 153 " --> pdb=" O LEU e 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA e 126 " --> pdb=" O LEU e 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU e 151 " --> pdb=" O ALA e 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL e 128 " --> pdb=" O SER e 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER e 149 " --> pdb=" O VAL e 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU e 148 " --> pdb=" O SER e 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL e 186 " --> pdb=" O LEU e 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA e 150 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER e 188 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA e 152 " --> pdb=" O SER e 188 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'f' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU f 194 " --> pdb=" O ARG f 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE f 223 " --> pdb=" O LEU f 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL f 196 " --> pdb=" O ILE f 223 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'f' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR f 245 " --> pdb=" O SER f 261 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER f 261 " --> pdb=" O TYR f 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG f 247 " --> pdb=" O TRP f 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE f 258 " --> pdb=" O THR f 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET f 294 " --> pdb=" O PHE f 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU f 260 " --> pdb=" O MET f 294 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'f' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL f 323 " --> pdb=" O GLN f 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA f 358 " --> pdb=" O VAL f 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE f 325 " --> pdb=" O ALA f 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU f 360 " --> pdb=" O PHE f 325 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE f 327 " --> pdb=" O GLU f 360 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'g' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE g 58 " --> pdb=" O LEU g 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS g 25 " --> pdb=" O TYR g 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR g 56 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'g' and resid 123 through 130 removed outlier: 6.651A pdb=" N VAL g 153 " --> pdb=" O LEU g 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA g 126 " --> pdb=" O LEU g 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU g 151 " --> pdb=" O ALA g 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL g 128 " --> pdb=" O SER g 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER g 149 " --> pdb=" O VAL g 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU g 148 " --> pdb=" O SER g 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL g 186 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA g 150 " --> pdb=" O VAL g 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER g 188 " --> pdb=" O ALA g 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA g 152 " --> pdb=" O SER g 188 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'h' and resid 184 through 188 removed outlier: 6.360A pdb=" N LEU h 194 " --> pdb=" O ARG h 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE h 223 " --> pdb=" O LEU h 194 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL h 196 " --> pdb=" O ILE h 223 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'h' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR h 245 " --> pdb=" O SER h 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER h 261 " --> pdb=" O TYR h 245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG h 247 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE h 258 " --> pdb=" O THR h 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET h 294 " --> pdb=" O PHE h 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU h 260 " --> pdb=" O MET h 294 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'h' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL h 323 " --> pdb=" O GLN h 356 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA h 358 " --> pdb=" O VAL h 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE h 325 " --> pdb=" O ALA h 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU h 360 " --> pdb=" O PHE h 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE h 327 " --> pdb=" O GLU h 360 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'i' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE i 58 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS i 25 " --> pdb=" O TYR i 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR i 56 " --> pdb=" O LYS i 25 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'i' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL i 153 " --> pdb=" O LEU i 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA i 126 " --> pdb=" O LEU i 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU i 151 " --> pdb=" O ALA i 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL i 128 " --> pdb=" O SER i 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER i 149 " --> pdb=" O VAL i 128 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU i 148 " --> pdb=" O SER i 184 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL i 186 " --> pdb=" O LEU i 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA i 150 " --> pdb=" O VAL i 186 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER i 188 " --> pdb=" O ALA i 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA i 152 " --> pdb=" O SER i 188 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'j' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU j 194 " --> pdb=" O ARG j 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE j 223 " --> pdb=" O LEU j 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL j 196 " --> pdb=" O ILE j 223 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'j' and resid 245 through 249 removed outlier: 6.520A pdb=" N TYR j 245 " --> pdb=" O SER j 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER j 261 " --> pdb=" O TYR j 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG j 247 " --> pdb=" O TRP j 259 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE j 258 " --> pdb=" O THR j 292 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET j 294 " --> pdb=" O PHE j 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU j 260 " --> pdb=" O MET j 294 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'j' and resid 315 through 319 removed outlier: 6.520A pdb=" N VAL j 323 " --> pdb=" O GLN j 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA j 358 " --> pdb=" O VAL j 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE j 325 " --> pdb=" O ALA j 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU j 360 " --> pdb=" O PHE j 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE j 327 " --> pdb=" O GLU j 360 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'k' and resid 21 through 27 removed outlier: 6.549A pdb=" N ILE k 58 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS k 25 " --> pdb=" O TYR k 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR k 56 " --> pdb=" O LYS k 25 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'k' and resid 123 through 130 removed outlier: 6.652A pdb=" N VAL k 153 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA k 126 " --> pdb=" O LEU k 151 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU k 151 " --> pdb=" O ALA k 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL k 128 " --> pdb=" O SER k 149 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER k 149 " --> pdb=" O VAL k 128 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU k 148 " --> pdb=" O SER k 184 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL k 186 " --> pdb=" O LEU k 148 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA k 150 " --> pdb=" O VAL k 186 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER k 188 " --> pdb=" O ALA k 150 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA k 152 " --> pdb=" O SER k 188 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'l' and resid 184 through 188 removed outlier: 6.359A pdb=" N LEU l 194 " --> pdb=" O ARG l 221 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE l 223 " --> pdb=" O LEU l 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL l 196 " --> pdb=" O ILE l 223 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'l' and resid 245 through 249 removed outlier: 6.521A pdb=" N TYR l 245 " --> pdb=" O SER l 261 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER l 261 " --> pdb=" O TYR l 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG l 247 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE l 258 " --> pdb=" O THR l 292 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET l 294 " --> pdb=" O PHE l 258 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU l 260 " --> pdb=" O MET l 294 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'l' and resid 315 through 319 removed outlier: 6.521A pdb=" N VAL l 323 " --> pdb=" O GLN l 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA l 358 " --> pdb=" O VAL l 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE l 325 " --> pdb=" O ALA l 358 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU l 360 " --> pdb=" O PHE l 325 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE l 327 " --> pdb=" O GLU l 360 " (cutoff:3.500A) 3288 hydrogen bonds defined for protein. 9144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.44 Time building geometry restraints manager: 24.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16349 1.32 - 1.44: 16071 1.44 - 1.56: 41572 1.56 - 1.68: 0 1.68 - 1.80: 336 Bond restraints: 74328 Sorted by residual: bond pdb=" CA ASP F 166 " pdb=" C ASP F 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.67e+00 bond pdb=" CA ASP R 166 " pdb=" C ASP R 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.66e+00 bond pdb=" CA ASP 6 166 " pdb=" C ASP 6 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.65e+00 bond pdb=" CA ASP N 166 " pdb=" C ASP N 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" CA ASP c 166 " pdb=" C ASP c 166 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.59e+00 ... (remaining 74323 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.86: 2286 106.86 - 113.61: 39730 113.61 - 120.36: 30545 120.36 - 127.12: 27324 127.12 - 133.87: 747 Bond angle restraints: 100632 Sorted by residual: angle pdb=" C ARG F 141 " pdb=" N PRO F 142 " pdb=" CA PRO F 142 " ideal model delta sigma weight residual 119.66 127.08 -7.42 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG 0 141 " pdb=" N PRO 0 142 " pdb=" CA PRO 0 142 " ideal model delta sigma weight residual 119.66 127.08 -7.42 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG 2 141 " pdb=" N PRO 2 142 " pdb=" CA PRO 2 142 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG N 141 " pdb=" N PRO N 142 " pdb=" CA PRO N 142 " ideal model delta sigma weight residual 119.66 127.06 -7.40 7.20e-01 1.93e+00 1.06e+02 angle pdb=" C ARG B 141 " pdb=" N PRO B 142 " pdb=" CA PRO B 142 " ideal model delta sigma weight residual 119.66 127.05 -7.39 7.20e-01 1.93e+00 1.05e+02 ... (remaining 100627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 43080 13.43 - 26.85: 1726 26.85 - 40.28: 314 40.28 - 53.71: 288 53.71 - 67.13: 168 Dihedral angle restraints: 45576 sinusoidal: 18840 harmonic: 26736 Sorted by residual: dihedral pdb=" CG ARG C 280 " pdb=" CD ARG C 280 " pdb=" NE ARG C 280 " pdb=" CZ ARG C 280 " ideal model delta sinusoidal sigma weight residual 180.00 -144.86 -35.14 2 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CG ARG 7 280 " pdb=" CD ARG 7 280 " pdb=" NE ARG 7 280 " pdb=" CZ ARG 7 280 " ideal model delta sinusoidal sigma weight residual -180.00 -144.87 -35.13 2 1.50e+01 4.44e-03 7.06e+00 dihedral pdb=" CG ARG 5 280 " pdb=" CD ARG 5 280 " pdb=" NE ARG 5 280 " pdb=" CZ ARG 5 280 " ideal model delta sinusoidal sigma weight residual 180.00 -144.88 -35.12 2 1.50e+01 4.44e-03 7.06e+00 ... (remaining 45573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5432 0.045 - 0.090: 3697 0.090 - 0.135: 1407 0.135 - 0.180: 346 0.180 - 0.225: 62 Chirality restraints: 10944 Sorted by residual: chirality pdb=" CA ASN i 173 " pdb=" N ASN i 173 " pdb=" C ASN i 173 " pdb=" CB ASN i 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASN 4 173 " pdb=" N ASN 4 173 " pdb=" C ASN 4 173 " pdb=" CB ASN 4 173 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 10941 not shown) Planarity restraints: 13248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO C 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO Y 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO Y 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO Y 188 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU f 187 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO f 188 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO f 188 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO f 188 " -0.067 5.00e-02 4.00e+02 ... (remaining 13245 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 36172 2.96 - 3.45: 70443 3.45 - 3.93: 120116 3.93 - 4.42: 136135 4.42 - 4.90: 213399 Nonbonded interactions: 576265 Sorted by model distance: nonbonded pdb=" C ASP 0 28 " pdb=" OD1 ASP 0 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP H 28 " pdb=" OD1 ASP H 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP N 28 " pdb=" OD1 ASP N 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP g 28 " pdb=" OD1 ASP g 28 " model vdw 2.479 3.270 nonbonded pdb=" C ASP 6 28 " pdb=" OD1 ASP 6 28 " model vdw 2.479 3.270 ... (remaining 576260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 8.750 Check model and map are aligned: 0.810 Set scattering table: 0.510 Process input model: 150.070 Find NCS groups from input model: 4.180 Set up NCS constraints: 0.830 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.055 74328 Z= 0.822 Angle : 1.383 10.941 100632 Z= 0.967 Chirality : 0.066 0.225 10944 Planarity : 0.010 0.131 13248 Dihedral : 9.896 67.134 28296 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 1.07 % Allowed : 3.48 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.08), residues: 8976 helix: -0.38 (0.07), residues: 3720 sheet: -0.52 (0.12), residues: 2136 loop : -0.56 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP d 350 HIS 0.004 0.001 HIS l 249 PHE 0.020 0.003 PHE B 175 TYR 0.038 0.005 TYR 1 346 ARG 0.004 0.001 ARG l 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1526 time to evaluate : 6.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 24 LEU cc_start: 0.9137 (mt) cc_final: 0.8812 (mp) REVERT: 0 154 TYR cc_start: 0.8533 (m-80) cc_final: 0.7942 (m-80) REVERT: 1 193 MET cc_start: 0.7917 (ttm) cc_final: 0.7575 (ttm) REVERT: 1 294 MET cc_start: 0.8495 (mmm) cc_final: 0.7891 (mmp) REVERT: 3 294 MET cc_start: 0.8522 (mmm) cc_final: 0.8052 (mmp) REVERT: 4 111 GLN cc_start: 0.7203 (mt0) cc_final: 0.6805 (mt0) REVERT: 5 193 MET cc_start: 0.8241 (ttm) cc_final: 0.7464 (ttm) REVERT: 5 294 MET cc_start: 0.8646 (mmm) cc_final: 0.8229 (mmp) REVERT: 6 88 MET cc_start: 0.7397 (mtt) cc_final: 0.6975 (mtt) REVERT: 7 193 MET cc_start: 0.7896 (ttm) cc_final: 0.7587 (ttm) REVERT: 7 248 ILE cc_start: 0.9006 (mt) cc_final: 0.8708 (mt) REVERT: 9 175 SER cc_start: 0.8243 (p) cc_final: 0.7899 (t) REVERT: 9 176 LEU cc_start: 0.8521 (mt) cc_final: 0.8164 (mm) REVERT: 9 248 ILE cc_start: 0.8721 (mt) cc_final: 0.8519 (mt) REVERT: A 294 MET cc_start: 0.8615 (mmm) cc_final: 0.8262 (mmp) REVERT: A 350 TRP cc_start: 0.8373 (m100) cc_final: 0.8059 (m100) REVERT: B 24 LEU cc_start: 0.9187 (mt) cc_final: 0.8874 (mt) REVERT: B 34 GLU cc_start: 0.7481 (tp30) cc_final: 0.7245 (tp30) REVERT: B 88 MET cc_start: 0.7980 (mtt) cc_final: 0.7755 (mtm) REVERT: B 135 ASP cc_start: 0.6400 (p0) cc_final: 0.5938 (t0) REVERT: B 190 ARG cc_start: 0.7618 (ptt90) cc_final: 0.5461 (ptt-90) REVERT: C 279 LEU cc_start: 0.8754 (mt) cc_final: 0.8451 (mm) REVERT: C 350 TRP cc_start: 0.8301 (m100) cc_final: 0.7957 (m100) REVERT: D 24 LEU cc_start: 0.9214 (mt) cc_final: 0.8903 (mp) REVERT: F 88 MET cc_start: 0.8261 (mtt) cc_final: 0.7968 (mtt) REVERT: F 195 LEU cc_start: 0.9102 (mt) cc_final: 0.8875 (mt) REVERT: G 294 MET cc_start: 0.9105 (mmm) cc_final: 0.8843 (mmp) REVERT: H 40 GLN cc_start: 0.8029 (mt0) cc_final: 0.7781 (mt0) REVERT: J 40 GLN cc_start: 0.8221 (mt0) cc_final: 0.7793 (mt0) REVERT: J 88 MET cc_start: 0.7992 (mtt) cc_final: 0.7707 (mtt) REVERT: J 172 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7444 (tptp) REVERT: M 193 MET cc_start: 0.6932 (ttm) cc_final: 0.6601 (ttm) REVERT: M 294 MET cc_start: 0.9156 (mmm) cc_final: 0.8807 (mmm) REVERT: N 24 LEU cc_start: 0.9073 (mt) cc_final: 0.8868 (mt) REVERT: O 193 MET cc_start: 0.7121 (ttm) cc_final: 0.6783 (ttm) REVERT: O 350 TRP cc_start: 0.8019 (m100) cc_final: 0.7591 (m100) REVERT: P 111 GLN cc_start: 0.6999 (mt0) cc_final: 0.6723 (mt0) REVERT: R 138 GLU cc_start: 0.6228 (tt0) cc_final: 0.5921 (mp0) REVERT: S 173 LEU cc_start: 0.8973 (tp) cc_final: 0.8738 (tp) REVERT: S 294 MET cc_start: 0.9159 (mmm) cc_final: 0.8882 (mmp) REVERT: T 83 VAL cc_start: 0.8765 (t) cc_final: 0.8403 (p) REVERT: T 111 GLN cc_start: 0.8104 (mt0) cc_final: 0.7697 (mt0) REVERT: T 189 GLU cc_start: 0.8156 (pt0) cc_final: 0.7802 (pm20) REVERT: W 294 MET cc_start: 0.8733 (mmm) cc_final: 0.8494 (mmp) REVERT: W 359 ILE cc_start: 0.8315 (mt) cc_final: 0.7711 (mt) REVERT: X 111 GLN cc_start: 0.7704 (mt0) cc_final: 0.7364 (mt0) REVERT: Y 294 MET cc_start: 0.8876 (mmm) cc_final: 0.8342 (mmp) REVERT: Y 350 TRP cc_start: 0.8268 (m100) cc_final: 0.7981 (m100) REVERT: b 294 MET cc_start: 0.8129 (mmm) cc_final: 0.7415 (mmp) REVERT: d 248 ILE cc_start: 0.9039 (mt) cc_final: 0.8586 (mt) REVERT: d 279 LEU cc_start: 0.8896 (mt) cc_final: 0.8478 (mt) REVERT: e 111 GLN cc_start: 0.7292 (mt0) cc_final: 0.7061 (mt0) REVERT: e 163 GLN cc_start: 0.8354 (mt0) cc_final: 0.8003 (tp40) REVERT: f 294 MET cc_start: 0.8035 (mmm) cc_final: 0.7526 (mmp) REVERT: g 101 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6936 (mt-10) REVERT: g 111 GLN cc_start: 0.7052 (mt0) cc_final: 0.6810 (mt0) REVERT: g 154 TYR cc_start: 0.7995 (m-80) cc_final: 0.7783 (m-80) REVERT: h 193 MET cc_start: 0.8326 (ttm) cc_final: 0.7714 (ttp) REVERT: h 294 MET cc_start: 0.8556 (mmm) cc_final: 0.8241 (mmp) REVERT: i 82 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7287 (ttm-80) REVERT: k 111 GLN cc_start: 0.7421 (mt0) cc_final: 0.7067 (mt0) REVERT: l 175 SER cc_start: 0.7841 (p) cc_final: 0.7289 (t) REVERT: l 181 LYS cc_start: 0.6730 (pttp) cc_final: 0.6399 (pttt) REVERT: l 193 MET cc_start: 0.8219 (ttm) cc_final: 0.7884 (ttm) REVERT: l 294 MET cc_start: 0.8290 (mmm) cc_final: 0.7975 (mmp) outliers start: 0 outliers final: 0 residues processed: 1526 average time/residue: 0.8338 time to fit residues: 1989.3348 Evaluate side-chains 631 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 8.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 4.9990 chunk 673 optimal weight: 7.9990 chunk 373 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 359 optimal weight: 2.9990 chunk 696 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 423 optimal weight: 0.9980 chunk 518 optimal weight: 0.0070 chunk 806 optimal weight: 0.1980 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 111 GLN 0 163 GLN 0 173 ASN 2 173 ASN ** 2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 76 GLN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 139 ASN B 163 GLN B 173 ASN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 173 ASN F 173 ASN H 139 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN J 163 GLN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 40 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 ASN N 163 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN P 163 GLN ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN R 40 GLN R 173 ASN T 139 ASN ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 GLN ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 196 GLN f 219 ASN g 76 GLN g 173 ASN i 173 ASN k 118 GLN k 163 GLN ** k 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 74328 Z= 0.195 Angle : 0.560 9.349 100632 Z= 0.304 Chirality : 0.043 0.166 10944 Planarity : 0.005 0.047 13248 Dihedral : 3.832 22.166 10128 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.09 % Favored : 97.64 % Rotamer: Outliers : 0.01 % Allowed : 1.47 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.09), residues: 8976 helix: 0.97 (0.08), residues: 3888 sheet: -0.07 (0.12), residues: 2184 loop : -0.10 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 350 HIS 0.004 0.001 HIS Z 162 PHE 0.014 0.001 PHE 4 175 TYR 0.014 0.001 TYR C 195 ARG 0.022 0.001 ARG 5 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 927 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 LYS cc_start: 0.7791 (mptt) cc_final: 0.7529 (mptt) REVERT: 0 181 ASP cc_start: 0.6652 (t0) cc_final: 0.6270 (t0) REVERT: 1 175 SER cc_start: 0.8530 (m) cc_final: 0.8315 (p) REVERT: 1 294 MET cc_start: 0.8218 (mmm) cc_final: 0.7491 (mmp) REVERT: 2 118 GLN cc_start: 0.7799 (pt0) cc_final: 0.7497 (tt0) REVERT: 3 193 MET cc_start: 0.8274 (ttp) cc_final: 0.7111 (ptm) REVERT: 3 196 VAL cc_start: 0.8689 (t) cc_final: 0.8309 (m) REVERT: 4 141 ARG cc_start: 0.6171 (mmm-85) cc_final: 0.5968 (mmm160) REVERT: 5 175 SER cc_start: 0.7962 (t) cc_final: 0.7693 (t) REVERT: 5 294 MET cc_start: 0.8282 (mmm) cc_final: 0.7992 (mmp) REVERT: 6 34 GLU cc_start: 0.7987 (tp30) cc_final: 0.7757 (tp30) REVERT: 6 88 MET cc_start: 0.7371 (mtt) cc_final: 0.6975 (mtt) REVERT: 7 193 MET cc_start: 0.7481 (ttm) cc_final: 0.7045 (ttm) REVERT: 9 175 SER cc_start: 0.8214 (p) cc_final: 0.7594 (t) REVERT: 9 294 MET cc_start: 0.7789 (mmm) cc_final: 0.6018 (mmm) REVERT: A 294 MET cc_start: 0.8559 (mmm) cc_final: 0.8251 (mmp) REVERT: C 216 TYR cc_start: 0.6623 (t80) cc_final: 0.6411 (t80) REVERT: C 350 TRP cc_start: 0.8488 (m100) cc_final: 0.8140 (m100) REVERT: D 203 LYS cc_start: 0.8047 (pptt) cc_final: 0.7679 (pptt) REVERT: E 294 MET cc_start: 0.8697 (mmp) cc_final: 0.8104 (mmp) REVERT: F 88 MET cc_start: 0.8198 (mtt) cc_final: 0.7921 (mtt) REVERT: H 83 VAL cc_start: 0.8781 (t) cc_final: 0.8499 (p) REVERT: H 189 GLU cc_start: 0.7921 (pp20) cc_final: 0.7721 (pp20) REVERT: J 88 MET cc_start: 0.7790 (mtt) cc_final: 0.7580 (mtt) REVERT: J 118 GLN cc_start: 0.7176 (tt0) cc_final: 0.6940 (tt0) REVERT: K 232 ILE cc_start: 0.8965 (mt) cc_final: 0.8732 (mt) REVERT: L 181 ASP cc_start: 0.6606 (t0) cc_final: 0.6216 (t0) REVERT: M 324 THR cc_start: 0.8861 (m) cc_final: 0.8659 (p) REVERT: O 229 ASN cc_start: 0.7913 (t0) cc_final: 0.7400 (t0) REVERT: O 350 TRP cc_start: 0.8119 (m100) cc_final: 0.7751 (m100) REVERT: P 181 ASP cc_start: 0.6723 (t0) cc_final: 0.6406 (t0) REVERT: Q 294 MET cc_start: 0.8850 (mmp) cc_final: 0.8210 (mmp) REVERT: R 141 ARG cc_start: 0.7490 (mmt90) cc_final: 0.7189 (mmt90) REVERT: S 173 LEU cc_start: 0.8902 (tp) cc_final: 0.8616 (tp) REVERT: T 203 LYS cc_start: 0.6957 (pptt) cc_final: 0.6567 (pptt) REVERT: W 193 MET cc_start: 0.8206 (ttp) cc_final: 0.6932 (ptm) REVERT: W 294 MET cc_start: 0.8453 (mmm) cc_final: 0.8227 (mmp) REVERT: X 25 LYS cc_start: 0.6722 (ttmm) cc_final: 0.6378 (ttmt) REVERT: X 203 LYS cc_start: 0.7247 (pptt) cc_final: 0.6033 (tptp) REVERT: Y 294 MET cc_start: 0.8681 (mmm) cc_final: 0.8140 (mmp) REVERT: b 193 MET cc_start: 0.6961 (ttp) cc_final: 0.6455 (ptm) REVERT: b 294 MET cc_start: 0.7731 (mmm) cc_final: 0.7009 (mmp) REVERT: c 144 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8003 (mtmm) REVERT: d 193 MET cc_start: 0.7345 (ttp) cc_final: 0.5881 (ptm) REVERT: d 294 MET cc_start: 0.7986 (mmm) cc_final: 0.7422 (mmm) REVERT: e 174 SER cc_start: 0.9157 (p) cc_final: 0.8888 (p) REVERT: e 203 LYS cc_start: 0.7498 (pptt) cc_final: 0.6854 (pptt) REVERT: h 193 MET cc_start: 0.8074 (ttm) cc_final: 0.7775 (ttp) REVERT: h 294 MET cc_start: 0.8163 (mmm) cc_final: 0.7753 (mmp) REVERT: i 34 GLU cc_start: 0.7832 (tp30) cc_final: 0.7577 (tp30) REVERT: l 175 SER cc_start: 0.7835 (p) cc_final: 0.7513 (t) REVERT: l 294 MET cc_start: 0.8088 (mmm) cc_final: 0.7526 (mmp) outliers start: 1 outliers final: 0 residues processed: 928 average time/residue: 0.7801 time to fit residues: 1165.7656 Evaluate side-chains 544 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 6.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 671 optimal weight: 0.0470 chunk 549 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 807 optimal weight: 5.9990 chunk 872 optimal weight: 2.9990 chunk 719 optimal weight: 1.9990 chunk 801 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 chunk 648 optimal weight: 0.1980 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 111 GLN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 219 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 173 ASN M 229 ASN N 111 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN V 111 GLN ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 GLN Z 111 GLN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 74328 Z= 0.169 Angle : 0.497 9.138 100632 Z= 0.261 Chirality : 0.041 0.158 10944 Planarity : 0.004 0.059 13248 Dihedral : 3.806 22.731 10128 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.50 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8976 helix: 1.90 (0.08), residues: 3720 sheet: 0.13 (0.11), residues: 2184 loop : 0.23 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 7 350 HIS 0.007 0.001 HIS 7 249 PHE 0.018 0.001 PHE f 258 TYR 0.022 0.001 TYR Z 154 ARG 0.019 0.000 ARG a 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 805 time to evaluate : 6.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 181 ASP cc_start: 0.6666 (t0) cc_final: 0.6168 (t0) REVERT: 1 193 MET cc_start: 0.7816 (ttm) cc_final: 0.7510 (ttp) REVERT: 1 294 MET cc_start: 0.8214 (mmm) cc_final: 0.7449 (mmp) REVERT: 5 193 MET cc_start: 0.8240 (ttm) cc_final: 0.7987 (ttp) REVERT: 5 294 MET cc_start: 0.8254 (mmm) cc_final: 0.8044 (mmp) REVERT: 6 88 MET cc_start: 0.7298 (mtt) cc_final: 0.6804 (mtt) REVERT: 7 193 MET cc_start: 0.7542 (ttm) cc_final: 0.7258 (ttm) REVERT: 8 155 GLU cc_start: 0.7405 (pp20) cc_final: 0.7128 (tm-30) REVERT: 9 175 SER cc_start: 0.7555 (p) cc_final: 0.7217 (t) REVERT: 9 193 MET cc_start: 0.7606 (ttp) cc_final: 0.6843 (ptm) REVERT: A 226 ASN cc_start: 0.8149 (m-40) cc_final: 0.7819 (m-40) REVERT: A 230 LYS cc_start: 0.8026 (ptmt) cc_final: 0.7769 (ptmt) REVERT: A 294 MET cc_start: 0.8648 (mmm) cc_final: 0.8347 (mmp) REVERT: C 216 TYR cc_start: 0.6542 (t80) cc_final: 0.6301 (t80) REVERT: F 203 LYS cc_start: 0.7283 (pptt) cc_final: 0.6952 (pptt) REVERT: H 88 MET cc_start: 0.7788 (mtt) cc_final: 0.7569 (mtt) REVERT: H 189 GLU cc_start: 0.7954 (pp20) cc_final: 0.7682 (pp20) REVERT: J 88 MET cc_start: 0.7876 (mtt) cc_final: 0.7672 (mtt) REVERT: K 232 ILE cc_start: 0.8942 (mt) cc_final: 0.8655 (mt) REVERT: L 181 ASP cc_start: 0.6616 (t0) cc_final: 0.6072 (t0) REVERT: O 193 MET cc_start: 0.7014 (ttp) cc_final: 0.5659 (ptm) REVERT: O 229 ASN cc_start: 0.8055 (t0) cc_final: 0.7544 (t0) REVERT: O 350 TRP cc_start: 0.8356 (m100) cc_final: 0.7941 (m100) REVERT: P 141 ARG cc_start: 0.6939 (mtt90) cc_final: 0.6441 (mtp85) REVERT: Q 294 MET cc_start: 0.8753 (mmp) cc_final: 0.8409 (mmp) REVERT: R 141 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6697 (mtt-85) REVERT: S 294 MET cc_start: 0.8856 (mmp) cc_final: 0.8490 (mmp) REVERT: W 193 MET cc_start: 0.8186 (ttp) cc_final: 0.7595 (ttp) REVERT: W 205 LEU cc_start: 0.9232 (mt) cc_final: 0.9016 (mm) REVERT: W 359 ILE cc_start: 0.8247 (mt) cc_final: 0.7773 (mt) REVERT: X 25 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6943 (ttmt) REVERT: X 203 LYS cc_start: 0.7040 (pptt) cc_final: 0.6050 (tptp) REVERT: Y 294 MET cc_start: 0.8603 (mmm) cc_final: 0.8211 (mmp) REVERT: Z 73 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8388 (tttm) REVERT: a 163 GLN cc_start: 0.7604 (mm110) cc_final: 0.7017 (mm110) REVERT: b 294 MET cc_start: 0.7977 (mmm) cc_final: 0.7290 (mmp) REVERT: b 324 THR cc_start: 0.9170 (p) cc_final: 0.8916 (t) REVERT: c 144 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8334 (mtmm) REVERT: d 294 MET cc_start: 0.8055 (mmm) cc_final: 0.7317 (mmp) REVERT: e 203 LYS cc_start: 0.7547 (pptt) cc_final: 0.6933 (pptt) REVERT: h 193 MET cc_start: 0.8196 (ttm) cc_final: 0.7774 (ttp) REVERT: h 294 MET cc_start: 0.8141 (mmm) cc_final: 0.7580 (mmt) REVERT: i 34 GLU cc_start: 0.7880 (tp30) cc_final: 0.7580 (tp30) REVERT: i 88 MET cc_start: 0.7398 (mtt) cc_final: 0.6948 (mtt) REVERT: k 34 GLU cc_start: 0.7839 (tp30) cc_final: 0.7512 (mm-30) REVERT: k 56 TYR cc_start: 0.8947 (m-80) cc_final: 0.8480 (m-80) REVERT: k 203 LYS cc_start: 0.7605 (pptt) cc_final: 0.7357 (pptt) REVERT: l 175 SER cc_start: 0.7868 (p) cc_final: 0.7532 (t) REVERT: l 193 MET cc_start: 0.8565 (ttp) cc_final: 0.7607 (ptm) REVERT: l 294 MET cc_start: 0.8056 (mmm) cc_final: 0.7423 (mmp) outliers start: 0 outliers final: 0 residues processed: 805 average time/residue: 0.8642 time to fit residues: 1115.1681 Evaluate side-chains 521 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 6.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 419 optimal weight: 8.9990 chunk 89 optimal weight: 0.0000 chunk 385 optimal weight: 10.0000 chunk 542 optimal weight: 0.9990 chunk 810 optimal weight: 9.9990 chunk 858 optimal weight: 5.9990 chunk 423 optimal weight: 3.9990 chunk 768 optimal weight: 3.9990 chunk 231 optimal weight: 0.0170 overall best weight: 1.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 173 ASN 2 173 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 249 HIS ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS D 173 ASN F 139 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 HIS ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN J 118 GLN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 ASN M 229 ASN N 162 HIS ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 40 GLN e 76 GLN ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 GLN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 74328 Z= 0.200 Angle : 0.493 9.385 100632 Z= 0.256 Chirality : 0.041 0.158 10944 Planarity : 0.004 0.053 13248 Dihedral : 3.766 21.448 10128 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.54 % Favored : 97.19 % Rotamer: Outliers : 0.01 % Allowed : 1.38 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.09), residues: 8976 helix: 2.19 (0.08), residues: 3696 sheet: 0.25 (0.11), residues: 2184 loop : 0.30 (0.10), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP j 350 HIS 0.007 0.001 HIS j 249 PHE 0.013 0.001 PHE F 65 TYR 0.017 0.001 TYR l 216 ARG 0.007 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 687 time to evaluate : 7.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 181 ASP cc_start: 0.6882 (t0) cc_final: 0.6393 (t0) REVERT: 1 219 ASN cc_start: 0.6595 (p0) cc_final: 0.5405 (p0) REVERT: 1 294 MET cc_start: 0.8163 (mmm) cc_final: 0.7488 (mmp) REVERT: 2 141 ARG cc_start: 0.6698 (mmm-85) cc_final: 0.6274 (mmm160) REVERT: 5 294 MET cc_start: 0.8360 (mmm) cc_final: 0.8050 (mmp) REVERT: 6 41 MET cc_start: 0.7525 (tmm) cc_final: 0.6811 (tmm) REVERT: 6 88 MET cc_start: 0.7228 (mtt) cc_final: 0.6653 (mtt) REVERT: 7 193 MET cc_start: 0.7687 (ttm) cc_final: 0.7361 (ttm) REVERT: 8 155 GLU cc_start: 0.7624 (pp20) cc_final: 0.7286 (tm-30) REVERT: 9 175 SER cc_start: 0.7641 (p) cc_final: 0.7223 (t) REVERT: 9 294 MET cc_start: 0.7883 (mmm) cc_final: 0.6795 (mmm) REVERT: A 294 MET cc_start: 0.8668 (mmm) cc_final: 0.8399 (mmp) REVERT: B 41 MET cc_start: 0.8085 (tmm) cc_final: 0.7856 (tmm) REVERT: C 193 MET cc_start: 0.8339 (ttp) cc_final: 0.7592 (ptm) REVERT: C 216 TYR cc_start: 0.6505 (t80) cc_final: 0.6293 (t80) REVERT: D 154 TYR cc_start: 0.7705 (m-80) cc_final: 0.7437 (m-80) REVERT: E 200 ASN cc_start: 0.9177 (t0) cc_final: 0.8972 (t0) REVERT: F 88 MET cc_start: 0.8485 (mtp) cc_final: 0.8249 (mtt) REVERT: F 154 TYR cc_start: 0.8371 (m-80) cc_final: 0.8162 (m-80) REVERT: F 203 LYS cc_start: 0.7269 (pptt) cc_final: 0.6905 (pptt) REVERT: H 88 MET cc_start: 0.7904 (mtt) cc_final: 0.7617 (mtt) REVERT: J 88 MET cc_start: 0.7846 (mtt) cc_final: 0.7579 (mtt) REVERT: J 118 GLN cc_start: 0.7730 (tt0) cc_final: 0.7303 (tt0) REVERT: L 181 ASP cc_start: 0.6853 (t0) cc_final: 0.6359 (t0) REVERT: O 350 TRP cc_start: 0.8464 (m100) cc_final: 0.8050 (m100) REVERT: P 141 ARG cc_start: 0.6702 (mtt90) cc_final: 0.6314 (ttm110) REVERT: S 294 MET cc_start: 0.8702 (mmp) cc_final: 0.8466 (mmp) REVERT: W 193 MET cc_start: 0.8631 (ttp) cc_final: 0.7897 (ttp) REVERT: X 203 LYS cc_start: 0.6895 (pptt) cc_final: 0.5825 (tptp) REVERT: Y 294 MET cc_start: 0.8638 (mmm) cc_final: 0.8298 (mmp) REVERT: a 41 MET cc_start: 0.7480 (tmm) cc_final: 0.6783 (tmm) REVERT: b 294 MET cc_start: 0.8079 (mmm) cc_final: 0.7497 (mmp) REVERT: c 25 LYS cc_start: 0.8275 (mttm) cc_final: 0.8063 (mptt) REVERT: d 193 MET cc_start: 0.7493 (ttp) cc_final: 0.6727 (ptm) REVERT: d 294 MET cc_start: 0.8149 (mmm) cc_final: 0.7480 (mmp) REVERT: e 141 ARG cc_start: 0.6487 (mmm-85) cc_final: 0.6217 (mmm160) REVERT: e 154 TYR cc_start: 0.8075 (m-80) cc_final: 0.7611 (m-80) REVERT: e 203 LYS cc_start: 0.7767 (pptt) cc_final: 0.7303 (pptt) REVERT: f 349 THR cc_start: 0.8728 (m) cc_final: 0.7863 (t) REVERT: h 193 MET cc_start: 0.8276 (ttm) cc_final: 0.7909 (ttp) REVERT: h 294 MET cc_start: 0.8105 (mmm) cc_final: 0.7884 (mmp) REVERT: i 34 GLU cc_start: 0.7885 (tp30) cc_final: 0.7576 (tp30) REVERT: i 88 MET cc_start: 0.7519 (mtt) cc_final: 0.7190 (mtt) REVERT: k 203 LYS cc_start: 0.7711 (pptt) cc_final: 0.7339 (pptt) REVERT: l 175 SER cc_start: 0.7852 (p) cc_final: 0.7472 (t) REVERT: l 294 MET cc_start: 0.8038 (mmm) cc_final: 0.7436 (mmp) outliers start: 1 outliers final: 1 residues processed: 688 average time/residue: 0.7840 time to fit residues: 868.7304 Evaluate side-chains 496 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 495 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 3.9990 chunk 487 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 639 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 732 optimal weight: 0.9980 chunk 593 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 438 optimal weight: 2.9990 chunk 770 optimal weight: 3.9990 chunk 216 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 173 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 173 ASN D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 ASN M 229 ASN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 ASN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 162 HIS i 173 ASN k 173 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 74328 Z= 0.137 Angle : 0.456 8.431 100632 Z= 0.235 Chirality : 0.041 0.195 10944 Planarity : 0.003 0.035 13248 Dihedral : 3.665 19.270 10128 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.52 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.09), residues: 8976 helix: 2.40 (0.08), residues: 3696 sheet: 0.39 (0.11), residues: 2184 loop : 0.34 (0.10), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 259 HIS 0.006 0.001 HIS 3 249 PHE 0.015 0.001 PHE 9 258 TYR 0.017 0.001 TYR D 154 ARG 0.007 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 6.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 56 TYR cc_start: 0.8813 (m-80) cc_final: 0.8477 (m-80) REVERT: 0 181 ASP cc_start: 0.6833 (t0) cc_final: 0.6308 (t0) REVERT: 1 294 MET cc_start: 0.8107 (mmm) cc_final: 0.7454 (mmp) REVERT: 2 163 GLN cc_start: 0.8030 (mm110) cc_final: 0.7716 (tp40) REVERT: 5 294 MET cc_start: 0.8369 (mmm) cc_final: 0.8057 (mmp) REVERT: 6 41 MET cc_start: 0.7745 (tmm) cc_final: 0.6873 (tmm) REVERT: 6 88 MET cc_start: 0.7362 (mtt) cc_final: 0.6824 (mtt) REVERT: 6 144 LYS cc_start: 0.8707 (mppt) cc_final: 0.8472 (mtmm) REVERT: 8 155 GLU cc_start: 0.7859 (pp20) cc_final: 0.7477 (tm-30) REVERT: 9 175 SER cc_start: 0.7638 (p) cc_final: 0.7295 (t) REVERT: 9 193 MET cc_start: 0.7997 (ttp) cc_final: 0.6602 (ptm) REVERT: 9 294 MET cc_start: 0.7738 (mmm) cc_final: 0.6627 (mmp) REVERT: A 294 MET cc_start: 0.8686 (mmm) cc_final: 0.8383 (mmp) REVERT: C 193 MET cc_start: 0.8370 (ttp) cc_final: 0.7648 (ptm) REVERT: C 216 TYR cc_start: 0.6680 (t80) cc_final: 0.6449 (t80) REVERT: D 73 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8191 (tttm) REVERT: D 154 TYR cc_start: 0.7834 (m-80) cc_final: 0.7554 (m-80) REVERT: F 25 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8256 (tttp) REVERT: F 88 MET cc_start: 0.7937 (mtt) cc_final: 0.7711 (mtt) REVERT: F 203 LYS cc_start: 0.7249 (pptt) cc_final: 0.6877 (pptt) REVERT: H 88 MET cc_start: 0.7855 (mtt) cc_final: 0.7536 (mtt) REVERT: H 120 MET cc_start: 0.8266 (mtp) cc_final: 0.7858 (ttm) REVERT: J 88 MET cc_start: 0.7788 (mtt) cc_final: 0.7499 (mtt) REVERT: K 294 MET cc_start: 0.8740 (mmp) cc_final: 0.8407 (mmm) REVERT: L 181 ASP cc_start: 0.6794 (t0) cc_final: 0.6410 (t0) REVERT: O 350 TRP cc_start: 0.8505 (m100) cc_final: 0.8089 (m100) REVERT: P 25 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7709 (tmtt) REVERT: Q 359 ILE cc_start: 0.8298 (mt) cc_final: 0.7670 (mt) REVERT: V 102 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8224 (mptt) REVERT: W 193 MET cc_start: 0.8539 (ttp) cc_final: 0.7904 (ttp) REVERT: Y 294 MET cc_start: 0.8608 (mmm) cc_final: 0.8278 (mmp) REVERT: a 41 MET cc_start: 0.7509 (tmm) cc_final: 0.6610 (tmm) REVERT: a 139 ASN cc_start: 0.6484 (p0) cc_final: 0.6106 (p0) REVERT: a 154 TYR cc_start: 0.7961 (m-80) cc_final: 0.7708 (m-10) REVERT: b 294 MET cc_start: 0.8096 (mmm) cc_final: 0.7543 (mmp) REVERT: c 25 LYS cc_start: 0.8337 (mttm) cc_final: 0.7900 (mptt) REVERT: c 144 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8365 (mtmm) REVERT: d 294 MET cc_start: 0.8097 (mmm) cc_final: 0.7460 (mmp) REVERT: e 154 TYR cc_start: 0.8069 (m-80) cc_final: 0.7713 (m-80) REVERT: e 203 LYS cc_start: 0.7856 (pptt) cc_final: 0.7453 (pptt) REVERT: f 184 PHE cc_start: 0.8222 (m-80) cc_final: 0.7638 (m-10) REVERT: f 349 THR cc_start: 0.8800 (m) cc_final: 0.7605 (t) REVERT: h 193 MET cc_start: 0.8261 (ttm) cc_final: 0.7957 (ttp) REVERT: i 34 GLU cc_start: 0.7827 (tp30) cc_final: 0.7395 (tp30) REVERT: i 88 MET cc_start: 0.7526 (mtt) cc_final: 0.7203 (mtt) REVERT: k 203 LYS cc_start: 0.7755 (pptt) cc_final: 0.7329 (pptt) REVERT: l 175 SER cc_start: 0.7798 (p) cc_final: 0.7448 (t) REVERT: l 193 MET cc_start: 0.8694 (ttp) cc_final: 0.7239 (ptm) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.7863 time to fit residues: 833.9979 Evaluate side-chains 483 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 6.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 6.9990 chunk 772 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 503 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 859 optimal weight: 2.9990 chunk 713 optimal weight: 3.9990 chunk 397 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 451 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN 4 111 GLN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 219 ASN J 162 HIS ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS L 173 ASN M 229 ASN N 40 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 HIS ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 111 GLN ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 219 ASN ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 194 GLN h 219 ASN i 173 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 74328 Z= 0.171 Angle : 0.466 6.506 100632 Z= 0.239 Chirality : 0.041 0.154 10944 Planarity : 0.003 0.039 13248 Dihedral : 3.658 19.402 10128 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.76 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 8976 helix: 2.47 (0.08), residues: 3696 sheet: 0.48 (0.11), residues: 2040 loop : 0.31 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 350 HIS 0.005 0.001 HIS 0 42 PHE 0.012 0.001 PHE N 65 TYR 0.009 0.001 TYR A 195 ARG 0.006 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 6.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 MET cc_start: 0.7484 (tmm) cc_final: 0.6440 (tmm) REVERT: 0 56 TYR cc_start: 0.8816 (m-80) cc_final: 0.8488 (m-80) REVERT: 0 181 ASP cc_start: 0.7046 (t0) cc_final: 0.6517 (t0) REVERT: 1 294 MET cc_start: 0.8091 (mmm) cc_final: 0.7475 (mmp) REVERT: 3 193 MET cc_start: 0.8430 (ttp) cc_final: 0.7788 (ptm) REVERT: 5 294 MET cc_start: 0.8198 (mmm) cc_final: 0.7906 (mmp) REVERT: 6 41 MET cc_start: 0.8047 (tmm) cc_final: 0.6920 (tmm) REVERT: 6 88 MET cc_start: 0.7454 (mtt) cc_final: 0.6914 (mtt) REVERT: 6 144 LYS cc_start: 0.8720 (mppt) cc_final: 0.8480 (mtmm) REVERT: 7 294 MET cc_start: 0.8347 (mtp) cc_final: 0.7882 (mtm) REVERT: 8 155 GLU cc_start: 0.7889 (pp20) cc_final: 0.7400 (tm-30) REVERT: 8 163 GLN cc_start: 0.8105 (mm110) cc_final: 0.7871 (mm-40) REVERT: 9 175 SER cc_start: 0.7683 (p) cc_final: 0.7333 (t) REVERT: 9 193 MET cc_start: 0.7968 (ttp) cc_final: 0.7190 (ptm) REVERT: 9 294 MET cc_start: 0.7679 (mmm) cc_final: 0.6732 (mmp) REVERT: A 294 MET cc_start: 0.8656 (mmm) cc_final: 0.8333 (mmm) REVERT: B 41 MET cc_start: 0.8293 (tmm) cc_final: 0.7924 (tmm) REVERT: C 216 TYR cc_start: 0.6746 (t80) cc_final: 0.6510 (t80) REVERT: F 25 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8303 (tttp) REVERT: F 88 MET cc_start: 0.7919 (mtt) cc_final: 0.7690 (mtt) REVERT: H 88 MET cc_start: 0.7733 (mtt) cc_final: 0.7189 (mtt) REVERT: H 102 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8287 (mmtm) REVERT: H 120 MET cc_start: 0.8306 (mtp) cc_final: 0.7918 (ttm) REVERT: L 181 ASP cc_start: 0.6829 (t0) cc_final: 0.6453 (t0) REVERT: P 25 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7746 (tmtt) REVERT: P 163 GLN cc_start: 0.8017 (mm110) cc_final: 0.7614 (mm-40) REVERT: P 203 LYS cc_start: 0.7265 (pptt) cc_final: 0.7007 (pptt) REVERT: S 205 LEU cc_start: 0.9452 (mt) cc_final: 0.9214 (mm) REVERT: T 88 MET cc_start: 0.7584 (mtt) cc_final: 0.7220 (mtt) REVERT: V 88 MET cc_start: 0.7675 (ptp) cc_final: 0.7302 (ptp) REVERT: W 193 MET cc_start: 0.8740 (ttp) cc_final: 0.8180 (ttp) REVERT: Y 294 MET cc_start: 0.8588 (mmm) cc_final: 0.8292 (mmp) REVERT: a 41 MET cc_start: 0.7730 (tmm) cc_final: 0.6630 (tmm) REVERT: a 154 TYR cc_start: 0.7974 (m-80) cc_final: 0.7718 (m-10) REVERT: b 294 MET cc_start: 0.8012 (mmm) cc_final: 0.7596 (mmp) REVERT: c 25 LYS cc_start: 0.8407 (mttm) cc_final: 0.7932 (mptt) REVERT: c 41 MET cc_start: 0.8409 (tmm) cc_final: 0.8179 (tmm) REVERT: c 144 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8463 (mtmm) REVERT: d 294 MET cc_start: 0.8192 (mmm) cc_final: 0.7266 (mmp) REVERT: e 141 ARG cc_start: 0.6319 (mmm-85) cc_final: 0.6005 (mmm160) REVERT: e 203 LYS cc_start: 0.7477 (pptt) cc_final: 0.7152 (pptt) REVERT: h 193 MET cc_start: 0.8240 (ttm) cc_final: 0.7980 (ttp) REVERT: i 34 GLU cc_start: 0.7786 (tp30) cc_final: 0.7425 (tp30) REVERT: i 41 MET cc_start: 0.7817 (tmm) cc_final: 0.6890 (tmm) REVERT: i 88 MET cc_start: 0.7553 (mtt) cc_final: 0.7201 (mtt) REVERT: j 294 MET cc_start: 0.8357 (mtp) cc_final: 0.7978 (mtm) REVERT: k 34 GLU cc_start: 0.7798 (tp30) cc_final: 0.7506 (mm-30) REVERT: k 41 MET cc_start: 0.7848 (tmm) cc_final: 0.7550 (tmm) REVERT: l 175 SER cc_start: 0.7822 (p) cc_final: 0.7435 (t) REVERT: l 193 MET cc_start: 0.8739 (ttp) cc_final: 0.7202 (ptm) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.7903 time to fit residues: 806.2624 Evaluate side-chains 485 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 6.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 489 optimal weight: 3.9990 chunk 627 optimal weight: 0.9990 chunk 486 optimal weight: 7.9990 chunk 723 optimal weight: 9.9990 chunk 479 optimal weight: 0.0370 chunk 855 optimal weight: 9.9990 chunk 535 optimal weight: 6.9990 chunk 521 optimal weight: 0.9990 chunk 395 optimal weight: 2.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 162 HIS ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 162 HIS ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN F 162 HIS ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 219 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN V 162 HIS ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 219 ASN g 162 HIS ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 74328 Z= 0.145 Angle : 0.459 9.145 100632 Z= 0.235 Chirality : 0.041 0.204 10944 Planarity : 0.003 0.036 13248 Dihedral : 3.640 22.261 10128 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.76 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.09), residues: 8976 helix: 2.54 (0.08), residues: 3696 sheet: 0.56 (0.11), residues: 2040 loop : 0.30 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 206 HIS 0.004 0.001 HIS W 249 PHE 0.011 0.001 PHE d 325 TYR 0.009 0.001 TYR O 216 ARG 0.007 0.000 ARG R 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 6.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 MET cc_start: 0.7798 (tmm) cc_final: 0.6721 (tmm) REVERT: 0 181 ASP cc_start: 0.7028 (t0) cc_final: 0.6452 (t0) REVERT: 1 193 MET cc_start: 0.8542 (tpp) cc_final: 0.8168 (tpp) REVERT: 1 294 MET cc_start: 0.8115 (mmm) cc_final: 0.7494 (mmp) REVERT: 5 294 MET cc_start: 0.8199 (mmm) cc_final: 0.7952 (mmp) REVERT: 6 41 MET cc_start: 0.8159 (tmm) cc_final: 0.6956 (tmm) REVERT: 6 88 MET cc_start: 0.7470 (mtt) cc_final: 0.6903 (mtt) REVERT: 6 144 LYS cc_start: 0.8748 (mppt) cc_final: 0.8487 (mtmm) REVERT: 7 294 MET cc_start: 0.8377 (mtp) cc_final: 0.7990 (mtm) REVERT: 8 155 GLU cc_start: 0.7865 (pp20) cc_final: 0.7496 (tm-30) REVERT: 9 175 SER cc_start: 0.7682 (p) cc_final: 0.7331 (t) REVERT: 9 193 MET cc_start: 0.8031 (ttp) cc_final: 0.7255 (ptm) REVERT: 9 294 MET cc_start: 0.7663 (mmm) cc_final: 0.6983 (mmm) REVERT: A 294 MET cc_start: 0.8560 (mmm) cc_final: 0.8297 (mmm) REVERT: B 41 MET cc_start: 0.8380 (tmm) cc_final: 0.7980 (tmm) REVERT: B 179 ASP cc_start: 0.8573 (p0) cc_final: 0.8173 (m-30) REVERT: C 193 MET cc_start: 0.7814 (ttp) cc_final: 0.7524 (tmm) REVERT: C 216 TYR cc_start: 0.6770 (t80) cc_final: 0.6512 (t80) REVERT: F 25 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8180 (tttp) REVERT: H 88 MET cc_start: 0.7602 (mtt) cc_final: 0.7133 (mtt) REVERT: H 102 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8230 (mmtm) REVERT: H 120 MET cc_start: 0.8266 (mtp) cc_final: 0.7992 (ttm) REVERT: J 40 GLN cc_start: 0.7478 (mt0) cc_final: 0.7114 (mt0) REVERT: L 141 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6964 (mmm160) REVERT: L 181 ASP cc_start: 0.6850 (t0) cc_final: 0.6427 (t0) REVERT: N 41 MET cc_start: 0.7771 (tmm) cc_final: 0.7400 (tmm) REVERT: P 163 GLN cc_start: 0.7987 (mm110) cc_final: 0.7599 (mm-40) REVERT: P 203 LYS cc_start: 0.7411 (pptt) cc_final: 0.7046 (pptt) REVERT: S 193 MET cc_start: 0.8029 (ttm) cc_final: 0.7661 (mmm) REVERT: S 219 ASN cc_start: 0.6219 (m-40) cc_final: 0.5778 (m-40) REVERT: T 88 MET cc_start: 0.7398 (mtt) cc_final: 0.7128 (mtt) REVERT: U 362 LYS cc_start: 0.8580 (ptmm) cc_final: 0.7858 (tttt) REVERT: V 88 MET cc_start: 0.7722 (ptp) cc_final: 0.7490 (ptp) REVERT: W 193 MET cc_start: 0.8824 (ttp) cc_final: 0.8007 (ttp) REVERT: W 219 ASN cc_start: 0.7924 (p0) cc_final: 0.7696 (p0) REVERT: Y 294 MET cc_start: 0.8568 (mmm) cc_final: 0.8331 (mmp) REVERT: a 41 MET cc_start: 0.7838 (tmm) cc_final: 0.6605 (tmm) REVERT: b 294 MET cc_start: 0.8011 (mmm) cc_final: 0.7624 (mmp) REVERT: c 25 LYS cc_start: 0.8372 (mttm) cc_final: 0.7948 (mptt) REVERT: c 41 MET cc_start: 0.8462 (tmm) cc_final: 0.8092 (tmm) REVERT: d 294 MET cc_start: 0.8086 (mmm) cc_final: 0.7295 (mmp) REVERT: e 141 ARG cc_start: 0.6266 (mmm-85) cc_final: 0.6048 (mmm160) REVERT: e 154 TYR cc_start: 0.8085 (m-80) cc_final: 0.7393 (m-80) REVERT: e 200 THR cc_start: 0.8973 (p) cc_final: 0.8752 (t) REVERT: e 203 LYS cc_start: 0.7552 (pptt) cc_final: 0.7260 (pptt) REVERT: f 193 MET cc_start: 0.8428 (ttp) cc_final: 0.7745 (ptm) REVERT: g 139 ASN cc_start: 0.4628 (t0) cc_final: 0.4381 (t0) REVERT: h 193 MET cc_start: 0.8319 (ttm) cc_final: 0.7922 (ttp) REVERT: i 34 GLU cc_start: 0.7718 (tp30) cc_final: 0.7410 (tp30) REVERT: i 41 MET cc_start: 0.7900 (tmm) cc_final: 0.6832 (tmm) REVERT: i 88 MET cc_start: 0.7570 (mtt) cc_final: 0.7156 (mtt) REVERT: j 294 MET cc_start: 0.8212 (mtp) cc_final: 0.7827 (mtm) REVERT: k 41 MET cc_start: 0.7962 (tmm) cc_final: 0.7718 (tmm) REVERT: l 175 SER cc_start: 0.7803 (p) cc_final: 0.7444 (t) REVERT: l 193 MET cc_start: 0.8767 (ttp) cc_final: 0.7209 (ptm) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.7955 time to fit residues: 819.9889 Evaluate side-chains 488 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 6.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 511 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 544 optimal weight: 0.0970 chunk 583 optimal weight: 6.9990 chunk 423 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 672 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN 2 173 ASN ** 4 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 162 HIS ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 219 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN U 249 HIS ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 HIS ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN k 111 GLN k 173 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 74328 Z= 0.186 Angle : 0.472 8.247 100632 Z= 0.242 Chirality : 0.041 0.166 10944 Planarity : 0.003 0.042 13248 Dihedral : 3.657 23.303 10128 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.09), residues: 8976 helix: 2.51 (0.08), residues: 3720 sheet: 0.60 (0.11), residues: 2040 loop : 0.35 (0.10), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 259 HIS 0.005 0.001 HIS 2 162 PHE 0.022 0.001 PHE D 89 TYR 0.014 0.001 TYR 2 154 ARG 0.012 0.000 ARG P 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 6.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 MET cc_start: 0.8067 (tmm) cc_final: 0.7368 (tmm) REVERT: 0 181 ASP cc_start: 0.7041 (t0) cc_final: 0.6608 (t0) REVERT: 1 193 MET cc_start: 0.8495 (tpp) cc_final: 0.8280 (tpp) REVERT: 1 294 MET cc_start: 0.8290 (mmm) cc_final: 0.7708 (mmp) REVERT: 5 294 MET cc_start: 0.8199 (mmm) cc_final: 0.7953 (mmp) REVERT: 6 41 MET cc_start: 0.8275 (tmm) cc_final: 0.7383 (tmm) REVERT: 8 163 GLN cc_start: 0.7867 (mm110) cc_final: 0.7308 (mm-40) REVERT: 9 193 MET cc_start: 0.8083 (ttp) cc_final: 0.7294 (ptm) REVERT: 9 294 MET cc_start: 0.7732 (mmm) cc_final: 0.7066 (mmm) REVERT: A 294 MET cc_start: 0.8531 (mmm) cc_final: 0.8247 (mmm) REVERT: B 41 MET cc_start: 0.8212 (tmm) cc_final: 0.7724 (tmm) REVERT: B 179 ASP cc_start: 0.8513 (p0) cc_final: 0.8120 (m-30) REVERT: C 193 MET cc_start: 0.7937 (ttp) cc_final: 0.7634 (tmm) REVERT: C 216 TYR cc_start: 0.6870 (t80) cc_final: 0.6582 (t80) REVERT: F 25 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8185 (tttp) REVERT: H 88 MET cc_start: 0.7539 (mtt) cc_final: 0.7031 (mtt) REVERT: H 102 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8246 (mmtm) REVERT: H 120 MET cc_start: 0.8204 (mtp) cc_final: 0.7689 (ttm) REVERT: J 40 GLN cc_start: 0.7539 (mt0) cc_final: 0.7172 (mt0) REVERT: L 141 ARG cc_start: 0.7311 (mmm160) cc_final: 0.7094 (mmm160) REVERT: L 181 ASP cc_start: 0.6887 (t0) cc_final: 0.6409 (t0) REVERT: N 41 MET cc_start: 0.7933 (tmm) cc_final: 0.7715 (tmm) REVERT: N 179 ASP cc_start: 0.8503 (p0) cc_final: 0.8245 (m-30) REVERT: P 154 TYR cc_start: 0.8493 (m-80) cc_final: 0.7899 (m-80) REVERT: P 163 GLN cc_start: 0.7981 (mm110) cc_final: 0.7570 (mm-40) REVERT: Q 205 LEU cc_start: 0.9177 (mt) cc_final: 0.8971 (mm) REVERT: R 144 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8546 (mtmm) REVERT: T 88 MET cc_start: 0.7664 (mtt) cc_final: 0.7350 (mtt) REVERT: U 362 LYS cc_start: 0.8566 (ptmm) cc_final: 0.8067 (tttt) REVERT: V 88 MET cc_start: 0.7956 (ptp) cc_final: 0.7560 (ptp) REVERT: W 193 MET cc_start: 0.8860 (ttp) cc_final: 0.7908 (ttp) REVERT: X 181 ASP cc_start: 0.6507 (t0) cc_final: 0.6242 (t0) REVERT: Y 294 MET cc_start: 0.8627 (mmm) cc_final: 0.8391 (mmp) REVERT: Z 41 MET cc_start: 0.8042 (tmm) cc_final: 0.7667 (tmm) REVERT: a 41 MET cc_start: 0.8068 (tmm) cc_final: 0.6801 (tmm) REVERT: b 294 MET cc_start: 0.8013 (mmm) cc_final: 0.7684 (mmp) REVERT: c 25 LYS cc_start: 0.8406 (mttm) cc_final: 0.8011 (mptt) REVERT: c 41 MET cc_start: 0.8483 (tmm) cc_final: 0.7967 (tmm) REVERT: d 193 MET cc_start: 0.8345 (ttp) cc_final: 0.7905 (ttp) REVERT: d 294 MET cc_start: 0.8117 (mmm) cc_final: 0.7574 (mmm) REVERT: e 141 ARG cc_start: 0.6392 (mmm-85) cc_final: 0.6136 (mmm160) REVERT: e 200 THR cc_start: 0.8968 (p) cc_final: 0.8720 (t) REVERT: e 203 LYS cc_start: 0.7600 (pptt) cc_final: 0.7256 (pptt) REVERT: h 193 MET cc_start: 0.8093 (ttm) cc_final: 0.7833 (ttp) REVERT: i 34 GLU cc_start: 0.7777 (tp30) cc_final: 0.7456 (tp30) REVERT: i 41 MET cc_start: 0.8085 (tmm) cc_final: 0.6986 (tmm) REVERT: i 88 MET cc_start: 0.7585 (mtt) cc_final: 0.7289 (mtt) REVERT: k 41 MET cc_start: 0.7948 (tmm) cc_final: 0.7615 (tmm) REVERT: l 175 SER cc_start: 0.7892 (p) cc_final: 0.7565 (t) REVERT: l 193 MET cc_start: 0.8758 (ttp) cc_final: 0.7658 (ptm) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.7978 time to fit residues: 788.1427 Evaluate side-chains 502 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 6.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 1.9990 chunk 819 optimal weight: 0.8980 chunk 748 optimal weight: 1.9990 chunk 797 optimal weight: 7.9990 chunk 480 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 626 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 720 optimal weight: 6.9990 chunk 754 optimal weight: 3.9990 chunk 794 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 249 HIS 2 162 HIS 2 173 ASN 4 173 ASN ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 249 HIS ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 249 HIS ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 HIS ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 249 HIS ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 HIS ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 173 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 74328 Z= 0.227 Angle : 0.500 10.090 100632 Z= 0.257 Chirality : 0.042 0.189 10944 Planarity : 0.003 0.049 13248 Dihedral : 3.789 20.107 10128 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 0.01 % Allowed : 0.21 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.09), residues: 8976 helix: 2.46 (0.08), residues: 3720 sheet: 1.11 (0.12), residues: 1776 loop : 0.05 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 7 259 HIS 0.004 0.001 HIS J 147 PHE 0.010 0.001 PHE a 175 TYR 0.013 0.001 TYR 2 154 ARG 0.007 0.000 ARG P 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 602 time to evaluate : 6.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 MET cc_start: 0.8130 (tmm) cc_final: 0.7451 (tmm) REVERT: 0 181 ASP cc_start: 0.7110 (t0) cc_final: 0.6689 (t0) REVERT: 1 193 MET cc_start: 0.8547 (tpp) cc_final: 0.8264 (tpp) REVERT: 1 294 MET cc_start: 0.8237 (mmm) cc_final: 0.7811 (mmp) REVERT: 4 173 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8498 (t0) REVERT: 6 41 MET cc_start: 0.8310 (tmm) cc_final: 0.7438 (tmm) REVERT: 6 102 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7746 (mmtm) REVERT: 6 144 LYS cc_start: 0.8789 (mppt) cc_final: 0.8554 (mtmm) REVERT: 8 41 MET cc_start: 0.8129 (tmm) cc_final: 0.7674 (tmm) REVERT: 8 163 GLN cc_start: 0.7831 (mm110) cc_final: 0.7415 (mm-40) REVERT: 9 193 MET cc_start: 0.8130 (ttp) cc_final: 0.7331 (ptm) REVERT: 9 294 MET cc_start: 0.7922 (mmm) cc_final: 0.7073 (mmp) REVERT: B 41 MET cc_start: 0.8286 (tmm) cc_final: 0.7879 (tmm) REVERT: C 216 TYR cc_start: 0.6929 (t80) cc_final: 0.6668 (t80) REVERT: F 25 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8221 (tttp) REVERT: F 102 LYS cc_start: 0.8356 (mptt) cc_final: 0.8155 (mptt) REVERT: H 88 MET cc_start: 0.7640 (mtt) cc_final: 0.7162 (mtt) REVERT: H 120 MET cc_start: 0.8177 (mtp) cc_final: 0.7755 (ttm) REVERT: J 25 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8018 (tttm) REVERT: J 40 GLN cc_start: 0.7563 (mt0) cc_final: 0.7198 (mt0) REVERT: L 141 ARG cc_start: 0.7272 (mmm160) cc_final: 0.7037 (mmm160) REVERT: L 181 ASP cc_start: 0.6971 (t0) cc_final: 0.6498 (t0) REVERT: P 154 TYR cc_start: 0.8575 (m-80) cc_final: 0.8028 (m-80) REVERT: P 163 GLN cc_start: 0.7948 (mm110) cc_final: 0.7571 (mm-40) REVERT: R 144 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8583 (mtmm) REVERT: T 88 MET cc_start: 0.7612 (mtt) cc_final: 0.7319 (mtt) REVERT: U 362 LYS cc_start: 0.8485 (ptmm) cc_final: 0.8088 (tttt) REVERT: V 41 MET cc_start: 0.8169 (tmm) cc_final: 0.7748 (tmm) REVERT: V 88 MET cc_start: 0.7942 (ptp) cc_final: 0.7732 (ptp) REVERT: W 193 MET cc_start: 0.8799 (ttp) cc_final: 0.7760 (ttp) REVERT: X 181 ASP cc_start: 0.6880 (t0) cc_final: 0.6599 (t0) REVERT: Y 294 MET cc_start: 0.8602 (mmm) cc_final: 0.8382 (mmm) REVERT: Z 41 MET cc_start: 0.8381 (tmm) cc_final: 0.7701 (tmm) REVERT: a 41 MET cc_start: 0.8334 (tmm) cc_final: 0.7832 (tmm) REVERT: b 294 MET cc_start: 0.8023 (mmm) cc_final: 0.7630 (mmp) REVERT: c 41 MET cc_start: 0.8571 (tmm) cc_final: 0.7931 (tmm) REVERT: c 141 ARG cc_start: 0.6184 (mmm160) cc_final: 0.5556 (mtp85) REVERT: c 179 ASP cc_start: 0.8604 (p0) cc_final: 0.8233 (m-30) REVERT: d 193 MET cc_start: 0.8378 (ttp) cc_final: 0.7941 (ttp) REVERT: d 294 MET cc_start: 0.8175 (mmm) cc_final: 0.7517 (mmp) REVERT: d 359 ILE cc_start: 0.7956 (mt) cc_final: 0.7745 (mt) REVERT: e 200 THR cc_start: 0.8955 (p) cc_final: 0.8708 (t) REVERT: e 203 LYS cc_start: 0.7767 (pptt) cc_final: 0.7381 (pptt) REVERT: h 193 MET cc_start: 0.8025 (ttm) cc_final: 0.7709 (ttp) REVERT: i 34 GLU cc_start: 0.7790 (tp30) cc_final: 0.7441 (tp30) REVERT: i 41 MET cc_start: 0.8124 (tmm) cc_final: 0.7274 (tmm) REVERT: i 88 MET cc_start: 0.7656 (mtt) cc_final: 0.7374 (mtt) REVERT: k 41 MET cc_start: 0.8119 (tmm) cc_final: 0.7606 (tmm) REVERT: l 175 SER cc_start: 0.7872 (p) cc_final: 0.7560 (t) REVERT: l 193 MET cc_start: 0.8775 (ttp) cc_final: 0.7486 (ptm) outliers start: 1 outliers final: 0 residues processed: 603 average time/residue: 0.7859 time to fit residues: 765.0751 Evaluate side-chains 497 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 496 time to evaluate : 6.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 1.9990 chunk 843 optimal weight: 4.9990 chunk 514 optimal weight: 0.9990 chunk 400 optimal weight: 0.3980 chunk 586 optimal weight: 0.4980 chunk 884 optimal weight: 4.9990 chunk 814 optimal weight: 5.9990 chunk 704 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 544 optimal weight: 6.9990 chunk 431 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 139 ASN ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN k 173 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 74328 Z= 0.179 Angle : 0.478 8.014 100632 Z= 0.245 Chirality : 0.041 0.170 10944 Planarity : 0.003 0.047 13248 Dihedral : 3.756 19.095 10128 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.10 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.09), residues: 8976 helix: 2.49 (0.08), residues: 3720 sheet: 1.11 (0.12), residues: 1776 loop : 0.05 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP j 259 HIS 0.004 0.001 HIS J 147 PHE 0.013 0.001 PHE 6 89 TYR 0.016 0.001 TYR 5 195 ARG 0.010 0.000 ARG J 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 6.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 MET cc_start: 0.8166 (tmm) cc_final: 0.7725 (tmm) REVERT: 0 181 ASP cc_start: 0.7044 (t0) cc_final: 0.6605 (t0) REVERT: 1 193 MET cc_start: 0.8566 (tpp) cc_final: 0.8245 (tpp) REVERT: 1 294 MET cc_start: 0.8273 (mmm) cc_final: 0.7864 (mmp) REVERT: 6 41 MET cc_start: 0.8353 (tmm) cc_final: 0.7441 (tmm) REVERT: 6 144 LYS cc_start: 0.8804 (mppt) cc_final: 0.8573 (mtmm) REVERT: 8 41 MET cc_start: 0.8095 (tmm) cc_final: 0.7656 (tmm) REVERT: 8 163 GLN cc_start: 0.7843 (mm110) cc_final: 0.7400 (mm-40) REVERT: 9 193 MET cc_start: 0.8146 (ttp) cc_final: 0.7342 (ptm) REVERT: 9 294 MET cc_start: 0.7907 (mmm) cc_final: 0.7378 (mmp) REVERT: B 41 MET cc_start: 0.8270 (tmm) cc_final: 0.7887 (tmm) REVERT: C 216 TYR cc_start: 0.6948 (t80) cc_final: 0.6650 (t80) REVERT: D 141 ARG cc_start: 0.5933 (mmm160) cc_final: 0.5684 (mmm160) REVERT: E 226 ASN cc_start: 0.8774 (m-40) cc_final: 0.8494 (m-40) REVERT: H 88 MET cc_start: 0.7715 (mtt) cc_final: 0.7277 (mtt) REVERT: H 120 MET cc_start: 0.8134 (mtp) cc_final: 0.7762 (ttm) REVERT: J 40 GLN cc_start: 0.7667 (mt0) cc_final: 0.7356 (mt0) REVERT: L 141 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6999 (mmm160) REVERT: L 181 ASP cc_start: 0.6970 (t0) cc_final: 0.6503 (t0) REVERT: N 41 MET cc_start: 0.8299 (tmm) cc_final: 0.7980 (tmm) REVERT: P 163 GLN cc_start: 0.7890 (mm110) cc_final: 0.7539 (mm-40) REVERT: Q 237 ASP cc_start: 0.7266 (p0) cc_final: 0.7025 (p0) REVERT: R 144 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8564 (mtmm) REVERT: T 88 MET cc_start: 0.7633 (mtt) cc_final: 0.7392 (mtt) REVERT: U 362 LYS cc_start: 0.8464 (ptmm) cc_final: 0.7897 (tttt) REVERT: V 41 MET cc_start: 0.8116 (tmm) cc_final: 0.7684 (tmm) REVERT: W 193 MET cc_start: 0.8861 (ttp) cc_final: 0.7702 (ttp) REVERT: X 41 MET cc_start: 0.7969 (tmm) cc_final: 0.6817 (tmm) REVERT: X 181 ASP cc_start: 0.6879 (t0) cc_final: 0.6664 (t0) REVERT: Z 25 LYS cc_start: 0.8232 (mttm) cc_final: 0.7877 (mptt) REVERT: Z 41 MET cc_start: 0.8269 (tmm) cc_final: 0.7773 (tmm) REVERT: a 41 MET cc_start: 0.8306 (tmm) cc_final: 0.7800 (tmm) REVERT: b 294 MET cc_start: 0.8025 (mmm) cc_final: 0.7698 (mmp) REVERT: c 25 LYS cc_start: 0.8677 (mttp) cc_final: 0.8132 (mptt) REVERT: c 41 MET cc_start: 0.8758 (tmm) cc_final: 0.8176 (tmm) REVERT: c 141 ARG cc_start: 0.6306 (mmm160) cc_final: 0.5670 (mtp85) REVERT: c 179 ASP cc_start: 0.8509 (p0) cc_final: 0.8179 (m-30) REVERT: d 193 MET cc_start: 0.8459 (ttp) cc_final: 0.7908 (ttp) REVERT: d 294 MET cc_start: 0.8168 (mmm) cc_final: 0.7553 (mmp) REVERT: e 154 TYR cc_start: 0.8431 (m-80) cc_final: 0.7925 (m-80) REVERT: e 200 THR cc_start: 0.8892 (p) cc_final: 0.8653 (t) REVERT: e 203 LYS cc_start: 0.7779 (pptt) cc_final: 0.7402 (pptt) REVERT: g 56 TYR cc_start: 0.8863 (m-80) cc_final: 0.8509 (m-10) REVERT: h 193 MET cc_start: 0.7971 (ttm) cc_final: 0.7699 (ttp) REVERT: i 34 GLU cc_start: 0.7731 (tp30) cc_final: 0.7385 (tp30) REVERT: i 41 MET cc_start: 0.8088 (tmm) cc_final: 0.7183 (tmm) REVERT: i 88 MET cc_start: 0.7609 (mtt) cc_final: 0.7357 (mtt) REVERT: i 102 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7903 (mmtm) REVERT: i 144 LYS cc_start: 0.8835 (mppt) cc_final: 0.8554 (mtmm) REVERT: j 294 MET cc_start: 0.7527 (mtm) cc_final: 0.7252 (mtm) REVERT: k 41 MET cc_start: 0.8082 (tmm) cc_final: 0.7591 (tmm) REVERT: l 175 SER cc_start: 0.7904 (p) cc_final: 0.7558 (t) REVERT: l 193 MET cc_start: 0.8722 (ttp) cc_final: 0.7149 (ptm) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.7941 time to fit residues: 761.2529 Evaluate side-chains 497 residues out of total 7776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 6.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 0.3980 chunk 750 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 649 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 705 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 chunk 724 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 6 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN D 173 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 219 ASN i 173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.069962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.056558 restraints weight = 201832.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.058107 restraints weight = 133350.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.059224 restraints weight = 99387.302| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 74328 Z= 0.118 Angle : 0.462 10.477 100632 Z= 0.234 Chirality : 0.041 0.168 10944 Planarity : 0.003 0.034 13248 Dihedral : 3.653 21.301 10128 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.83 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.09), residues: 8976 helix: 2.52 (0.08), residues: 3744 sheet: 1.23 (0.12), residues: 1776 loop : 0.04 (0.10), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 259 HIS 0.006 0.001 HIS D 42 PHE 0.020 0.001 PHE J 89 TYR 0.010 0.001 TYR O 195 ARG 0.006 0.000 ARG P 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14879.85 seconds wall clock time: 262 minutes 59.76 seconds (15779.76 seconds total)