Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 26 14:17:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e82_31008/08_2023/7e82_31008.pdb" } resolution = 3.3 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= 0.078 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 352 5.16 5 C 62663 2.51 5 N 17762 2.21 5 O 20829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DF PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 101606 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "B" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "C" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "D" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "E" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "F" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "G" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "H" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "I" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "J" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "K" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1941 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain: "M" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1949 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "N" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1887 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 1 Chain: "O" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1894 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "P" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1862 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "Q" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1858 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 1 Chain: "R" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1875 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "S" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1858 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 1 Chain: "T" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1902 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 9, 'TRANS': 243} Chain breaks: 1 Chain: "U" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1941 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain: "a" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain: "b" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1804 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain: "c" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain: "d" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain: "e" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "5" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "7" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "9" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "f" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 936 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "g" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 949 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Chain: "h" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 935 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "j" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 931 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Chain: "l" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "m" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "o" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "p" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 940 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "8" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "i" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 944 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "k" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 852 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "n" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "V" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1941 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain: "W" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1941 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain: "X" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1941 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain: "q" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "r" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 526 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "s" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "t" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "v" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 289 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "DA" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DB" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DC" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DD" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DE" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DF" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DG" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DH" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DI" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DJ" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DK" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Time building chain proxies: 42.00, per 1000 atoms: 0.41 Number of scatterers: 101606 At special positions: 0 Unit cell: (190.822, 192.129, 373.802, 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 352 16.00 O 20829 8.00 N 17762 7.00 C 62663 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: 30.54 Conformation dependent library (CDL) restraints added in 11.3 seconds 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24884 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 380 sheets defined 27.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 removed outlier: 3.653A pdb=" N ASN A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.502A pdb=" N GLY A 183 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 259 removed outlier: 3.631A pdb=" N GLU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 28 removed outlier: 3.660A pdb=" N ASN B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 removed outlier: 4.190A pdb=" N ALA B 166 " --> pdb=" O GLY B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 225 through 259 removed outlier: 3.677A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 28 removed outlier: 3.633A pdb=" N ASN C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) 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 225 through 259 removed outlier: 3.842A pdb=" N GLU C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 230 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 28 removed outlier: 3.648A pdb=" N ASN D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 184 removed outlier: 3.541A pdb=" N LEU D 184 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 259 removed outlier: 3.647A pdb=" N LEU D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.681A pdb=" N ASN E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 225 through 259 removed outlier: 3.837A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.666A pdb=" N ASN F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 225 through 259 removed outlier: 3.773A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 28 removed outlier: 3.663A pdb=" N ASN G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 260 removed outlier: 4.082A pdb=" N GLU G 229 " --> pdb=" O ASN G 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU G 230 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU G 260 " --> pdb=" O LYS G 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 28 removed outlier: 3.846A pdb=" N THR H 10 " --> pdb=" O TRP H 6 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 28 " --> pdb=" O ASN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 184 Processing helix chain 'H' and resid 225 through 228 Processing helix chain 'H' and resid 229 through 259 removed outlier: 3.549A pdb=" N ALA H 246 " --> pdb=" O ILE H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 28 removed outlier: 3.598A pdb=" N ASN I 28 " --> pdb=" O ASN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 260 removed outlier: 3.718A pdb=" N GLU I 229 " --> pdb=" O ASN I 225 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU I 230 " --> pdb=" O VAL I 226 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL I 231 " --> pdb=" O ALA I 227 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU I 260 " --> pdb=" O LYS I 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 28 removed outlier: 3.983A pdb=" N THR J 10 " --> pdb=" O TRP J 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 184 Processing helix chain 'J' and resid 195 through 199 removed outlier: 3.836A pdb=" N GLY J 199 " --> pdb=" O GLN J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 258 removed outlier: 4.378A pdb=" N VAL J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 28 removed outlier: 3.769A pdb=" N THR K 10 " --> pdb=" O TRP K 6 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN K 28 " --> pdb=" O ASN K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 184 Processing helix chain 'K' and resid 225 through 260 removed outlier: 4.129A pdb=" N VAL K 231 " --> pdb=" O ALA K 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 28 removed outlier: 3.809A pdb=" N THR L 10 " --> pdb=" O TRP L 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN L 28 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 184 removed outlier: 3.670A pdb=" N GLY L 183 " --> pdb=" O ASN L 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 184 " --> pdb=" O ASP L 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 180 through 184' Processing helix chain 'L' and resid 225 through 259 removed outlier: 3.727A pdb=" N GLU L 229 " --> pdb=" O ASN L 225 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU L 230 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL L 231 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN L 259 " --> pdb=" O GLN L 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 28 removed outlier: 3.885A pdb=" N TRP M 6 " --> pdb=" O ILE M 2 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN M 28 " --> pdb=" O ASN M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 260 removed outlier: 4.013A pdb=" N VAL M 231 " --> pdb=" O ALA M 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 28 removed outlier: 3.729A pdb=" N ASN N 28 " --> pdb=" O ASN N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 184 Processing helix chain 'N' and resid 225 through 260 removed outlier: 3.830A pdb=" N GLU N 229 " --> pdb=" O ASN N 225 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU N 230 " --> pdb=" O VAL N 226 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL N 231 " --> pdb=" O ALA N 227 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU N 260 " --> pdb=" O LYS N 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 28 removed outlier: 3.693A pdb=" N THR O 10 " --> pdb=" O TRP O 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN O 28 " --> pdb=" O ASN O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 259 removed outlier: 3.590A pdb=" N VAL O 231 " --> pdb=" O ALA O 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 28 removed outlier: 3.718A pdb=" N ASN P 28 " --> pdb=" O ASN P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 260 removed outlier: 3.571A pdb=" N GLU P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU P 230 " --> pdb=" O VAL P 226 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL P 231 " --> pdb=" O ALA P 227 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU P 260 " --> pdb=" O LYS P 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 28 removed outlier: 3.970A pdb=" N ILE Q 7 " --> pdb=" O SER Q 3 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN Q 28 " --> pdb=" O ASN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 184 removed outlier: 3.535A pdb=" N GLY Q 183 " --> pdb=" O ASN Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 260 removed outlier: 4.182A pdb=" N VAL Q 231 " --> pdb=" O ALA Q 227 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA Q 246 " --> pdb=" O ILE Q 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL Q 247 " --> pdb=" O ASN Q 243 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU Q 260 " --> pdb=" O LYS Q 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 28 removed outlier: 4.371A pdb=" N ILE R 7 " --> pdb=" O SER R 3 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN R 28 " --> pdb=" O ASN R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 260 removed outlier: 3.866A pdb=" N LYS R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA R 246 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL R 247 " --> pdb=" O ASN R 243 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 260 " --> pdb=" O LYS R 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 28 removed outlier: 3.513A pdb=" N ASN S 28 " --> pdb=" O ASN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 260 removed outlier: 3.738A pdb=" N GLU S 229 " --> pdb=" O ASN S 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU S 230 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL S 231 " --> pdb=" O ALA S 227 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU S 260 " --> pdb=" O LYS S 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 28 removed outlier: 3.701A pdb=" N ASN T 28 " --> pdb=" O ASN T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 184 removed outlier: 3.693A pdb=" N GLY T 183 " --> pdb=" O ASN T 180 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 260 removed outlier: 3.651A pdb=" N LYS T 245 " --> pdb=" O GLU T 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 246 " --> pdb=" O ILE T 242 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL T 247 " --> pdb=" O ASN T 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 28 removed outlier: 3.564A pdb=" N ASN U 28 " --> pdb=" O ASN U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 184 removed outlier: 3.560A pdb=" N LEU U 184 " --> pdb=" O ASP U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 259 removed outlier: 3.527A pdb=" N VAL U 231 " --> pdb=" O ALA U 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 28 removed outlier: 4.247A pdb=" N THR a 7 " --> pdb=" O HIS a 3 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA a 8 " --> pdb=" O ALA a 4 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN a 28 " --> pdb=" O SER a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 155 Processing helix chain 'a' and resid 182 through 190 Processing helix chain 'a' and resid 212 through 242 Processing helix chain 'a' and resid 243 through 250 removed outlier: 4.347A pdb=" N MET a 250 " --> pdb=" O GLN a 246 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 28 removed outlier: 3.723A pdb=" N ASN b 28 " --> pdb=" O SER b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 155 removed outlier: 3.643A pdb=" N VAL b 155 " --> pdb=" O PRO b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 189 Processing helix chain 'b' and resid 212 through 245 Processing helix chain 'b' and resid 246 through 249 Processing helix chain 'c' and resid 2 through 2 No H-bonds generated for 'chain 'c' and resid 2 through 2' Processing helix chain 'c' and resid 3 through 28 removed outlier: 3.897A pdb=" N THR c 7 " --> pdb=" O HIS c 3 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA c 8 " --> pdb=" O ALA c 4 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN c 28 " --> pdb=" O SER c 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 155 removed outlier: 3.584A pdb=" N VAL c 155 " --> pdb=" O PRO c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 182 through 190 Processing helix chain 'c' and resid 212 through 245 Processing helix chain 'c' and resid 246 through 249 Processing helix chain 'd' and resid 3 through 28 removed outlier: 3.674A pdb=" N ASN d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 155 removed outlier: 3.588A pdb=" N VAL d 155 " --> pdb=" O PRO d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 190 Processing helix chain 'd' and resid 212 through 245 Processing helix chain 'd' and resid 246 through 249 Processing helix chain 'e' and resid 3 through 28 removed outlier: 3.552A pdb=" N THR e 7 " --> pdb=" O HIS e 3 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN e 28 " --> pdb=" O SER e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 155 removed outlier: 3.587A pdb=" N VAL e 155 " --> pdb=" O PRO e 152 " (cutoff:3.500A) Processing helix chain 'e' and resid 182 through 190 Processing helix chain 'e' and resid 212 through 245 Processing helix chain 'e' and resid 246 through 249 Processing helix chain 'f' and resid 4 through 30 removed outlier: 4.062A pdb=" N ASP f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 97 through 130 removed outlier: 3.783A pdb=" N LEU f 130 " --> pdb=" O MET f 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 30 removed outlier: 3.882A pdb=" N ASP g 8 " --> pdb=" O LEU g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 40 removed outlier: 3.669A pdb=" N GLN g 40 " --> pdb=" O PRO g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 130 removed outlier: 3.743A pdb=" N LEU g 130 " --> pdb=" O MET g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 134 removed outlier: 4.141A pdb=" N GLN g 134 " --> pdb=" O THR g 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 131 through 134' Processing helix chain 'h' and resid 4 through 30 removed outlier: 4.253A pdb=" N ASP h 8 " --> pdb=" O LEU h 4 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 130 removed outlier: 3.928A pdb=" N MET h 106 " --> pdb=" O MET h 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 30 removed outlier: 4.042A pdb=" N PHE j 7 " --> pdb=" O LEU j 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP j 8 " --> pdb=" O LEU j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 33 No H-bonds generated for 'chain 'j' and resid 31 through 33' Processing helix chain 'j' and resid 98 through 131 removed outlier: 3.548A pdb=" N MET j 106 " --> pdb=" O MET j 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR j 131 " --> pdb=" O LEU j 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 32 removed outlier: 3.614A pdb=" N LEU l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE l 11 " --> pdb=" O ALA l 7 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 44 through 54 Processing helix chain 'l' and resid 101 through 133 Processing helix chain 'm' and resid 4 through 32 removed outlier: 4.606A pdb=" N GLN m 12 " --> pdb=" O ALA m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 54 Processing helix chain 'm' and resid 102 through 134 removed outlier: 3.693A pdb=" N VAL m 133 " --> pdb=" O GLY m 129 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU m 134 " --> pdb=" O MET m 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 32 removed outlier: 4.665A pdb=" N GLN o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA o 15 " --> pdb=" O PHE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 44 through 55 Processing helix chain 'o' and resid 101 through 134 removed outlier: 3.715A pdb=" N VAL o 133 " --> pdb=" O GLY o 129 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU o 134 " --> pdb=" O MET o 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 30 removed outlier: 4.033A pdb=" N ASP p 8 " --> pdb=" O LEU p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 40 removed outlier: 3.867A pdb=" N GLN p 40 " --> pdb=" O PRO p 37 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 131 Processing helix chain 'i' and resid 4 through 30 removed outlier: 4.178A pdb=" N ASP i 8 " --> pdb=" O LEU i 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 130 Processing helix chain 'k' and resid 3 through 32 removed outlier: 3.994A pdb=" N ALA k 8 " --> pdb=" O ARG k 4 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE k 11 " --> pdb=" O ALA k 7 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN k 12 " --> pdb=" O ALA k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 53 Processing helix chain 'k' and resid 102 through 134 removed outlier: 3.612A pdb=" N LEU k 134 " --> pdb=" O MET k 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 32 removed outlier: 4.340A pdb=" N GLN n 12 " --> pdb=" O ALA n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 55 removed outlier: 3.612A pdb=" N VAL n 54 " --> pdb=" O LYS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 134 removed outlier: 3.751A pdb=" N LEU n 134 " --> pdb=" O MET n 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 28 removed outlier: 4.091A pdb=" N THR V 10 " --> pdb=" O TRP V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 260 removed outlier: 4.083A pdb=" N VAL V 231 " --> pdb=" O ALA V 227 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU V 260 " --> pdb=" O LYS V 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 28 removed outlier: 4.022A pdb=" N THR W 10 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN W 28 " --> pdb=" O ASN W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 184 Processing helix chain 'W' and resid 225 through 260 removed outlier: 3.652A pdb=" N VAL W 231 " --> pdb=" O ALA W 227 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 28 removed outlier: 3.892A pdb=" N THR X 10 " --> pdb=" O TRP X 6 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN X 28 " --> pdb=" O ASN X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 184 Processing helix chain 'X' and resid 225 through 259 removed outlier: 3.810A pdb=" N GLU X 229 " --> pdb=" O ASN X 225 " (cutoff:3.500A) Processing helix chain 'q' and resid 34 through 61 Processing helix chain 'q' and resid 70 through 101 Processing helix chain 'r' and resid 36 through 61 Processing helix chain 'r' and resid 69 through 101 Processing helix chain 's' and resid 34 through 61 Processing helix chain 's' and resid 67 through 101 Processing helix chain 't' and resid 34 through 61 Processing helix chain 't' and resid 70 through 101 Processing helix chain 'u' and resid 34 through 61 removed outlier: 3.819A pdb=" N LEU u 61 " --> pdb=" O GLU u 57 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 101 Processing helix chain 'v' and resid 67 through 102 Processing helix chain 'DA' and resid 3 through 26 Processing helix chain 'DA' and resid 174 through 178 Processing helix chain 'DA' and resid 367 through 402 removed outlier: 3.562A pdb=" N VALDA 373 " --> pdb=" O SERDA 369 " (cutoff:3.500A) Processing helix chain 'DB' and resid 3 through 26 Processing helix chain 'DB' and resid 367 through 402 removed outlier: 3.632A pdb=" N VALDB 373 " --> pdb=" O SERDB 369 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILEDB 389 " --> pdb=" O ASNDB 385 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEUDB 399 " --> pdb=" O ILEDB 395 " (cutoff:3.500A) Processing helix chain 'DC' and resid 3 through 26 Processing helix chain 'DC' and resid 367 through 402 removed outlier: 3.590A pdb=" N VALDC 373 " --> pdb=" O SERDC 369 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THRDC 388 " --> pdb=" O SERDC 384 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILEDC 389 " --> pdb=" O ASNDC 385 " (cutoff:3.500A) Processing helix chain 'DD' and resid 3 through 26 Processing helix chain 'DD' and resid 367 through 402 removed outlier: 3.701A pdb=" N ILEDD 389 " --> pdb=" O ASNDD 385 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEUDD 399 " --> pdb=" O ILEDD 395 " (cutoff:3.500A) Processing helix chain 'DE' and resid 3 through 26 removed outlier: 3.530A pdb=" N SERDE 8 " --> pdb=" O SERDE 4 " (cutoff:3.500A) Processing helix chain 'DE' and resid 367 through 402 removed outlier: 3.604A pdb=" N THRDE 388 " --> pdb=" O SERDE 384 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEDE 389 " --> pdb=" O ASNDE 385 " (cutoff:3.500A) Processing helix chain 'DF' and resid 3 through 26 Processing helix chain 'DF' and resid 367 through 402 removed outlier: 3.702A pdb=" N VALDF 373 " --> pdb=" O SERDF 369 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASNDF 374 " --> pdb=" O LYSDF 370 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEUDF 399 " --> pdb=" O ILEDF 395 " (cutoff:3.500A) Processing helix chain 'DG' and resid 5 through 26 Processing helix chain 'DG' and resid 174 through 178 removed outlier: 4.268A pdb=" N TYRDG 178 " --> pdb=" O ALADG 175 " (cutoff:3.500A) Processing helix chain 'DG' and resid 367 through 402 removed outlier: 3.568A pdb=" N VALDG 373 " --> pdb=" O SERDG 369 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALDG 377 " --> pdb=" O VALDG 373 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRDG 398 " --> pdb=" O GLNDG 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEUDG 399 " --> pdb=" O ILEDG 395 " (cutoff:3.500A) Processing helix chain 'DH' and resid 3 through 26 Processing helix chain 'DH' and resid 367 through 402 removed outlier: 3.894A pdb=" N VALDH 373 " --> pdb=" O SERDH 369 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEUDH 396 " --> pdb=" O GLNDH 392 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THRDH 398 " --> pdb=" O GLNDH 394 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEUDH 399 " --> pdb=" O ILEDH 395 " (cutoff:3.500A) Processing helix chain 'DI' and resid 3 through 26 Processing helix chain 'DI' and resid 367 through 402 removed outlier: 3.549A pdb=" N VALDI 373 " --> pdb=" O SERDI 369 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THRDI 388 " --> pdb=" O SERDI 384 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUDI 396 " --> pdb=" O GLNDI 392 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEUDI 399 " --> pdb=" O ILEDI 395 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 3 through 26 removed outlier: 3.575A pdb=" N ALADJ 13 " --> pdb=" O GLYDJ 9 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 367 through 402 removed outlier: 3.775A pdb=" N VALDJ 373 " --> pdb=" O SERDJ 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALADJ 386 " --> pdb=" O TYRDJ 382 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLNDJ 387 " --> pdb=" O GLNDJ 383 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THRDJ 388 " --> pdb=" O SERDJ 384 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEUDJ 399 " --> pdb=" O ILEDJ 395 " (cutoff:3.500A) Processing helix chain 'DK' and resid 3 through 26 removed outlier: 3.537A pdb=" N GLYDK 9 " --> pdb=" O GLNDK 5 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEUDK 10 " --> pdb=" O ALADK 6 " (cutoff:3.500A) Processing helix chain 'DK' and resid 174 through 178 removed outlier: 3.967A pdb=" N SERDK 177 " --> pdb=" O ASPDK 174 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYRDK 178 " --> pdb=" O ALADK 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'DK' and resid 174 through 178' Processing helix chain 'DK' and resid 367 through 401 removed outlier: 3.818A pdb=" N ALADK 386 " --> pdb=" O TYRDK 382 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THRDK 388 " --> pdb=" O SERDK 384 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEUDK 399 " --> pdb=" O ILEDK 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 43 removed outlier: 6.323A pdb=" N GLU A 42 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 50 removed outlier: 6.320A pdb=" N LEU A 66 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 115 removed outlier: 4.216A pdb=" N GLN A 135 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 136 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 128 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 151 removed outlier: 4.144A pdb=" N SER A 148 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 157 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.974A pdb=" N LEU A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 43 removed outlier: 5.849A pdb=" N ARG B 38 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 77 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 40 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.293A pdb=" N LEU B 66 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB2, first strand: chain 'B' and resid 95 through 98 Processing sheet with id=AB3, first strand: chain 'B' and resid 112 through 115 removed outlier: 4.315A pdb=" N GLN B 135 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 128 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.993A pdb=" N SER B 148 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 157 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 159 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 168 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.989A pdb=" N GLU B 185 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 193 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.704A pdb=" N ALA C 76 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C 42 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.372A pdb=" N LEU C 66 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AC1, first strand: chain 'C' and resid 95 through 98 Processing sheet with id=AC2, first strand: chain 'C' and resid 112 through 115 removed outlier: 4.158A pdb=" N GLN C 135 " --> pdb=" O MET C 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AC4, first strand: chain 'C' and resid 148 through 151 removed outlier: 7.260A pdb=" N VAL C 157 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 168 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AC6, first strand: chain 'C' and resid 184 through 187 removed outlier: 3.797A pdb=" N LEU C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 37 through 43 removed outlier: 5.522A pdb=" N ARG D 38 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR D 77 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 40 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 46 through 50 removed outlier: 6.586A pdb=" N LEU D 66 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 95 through 98 Processing sheet with id=AD1, first strand: chain 'D' and resid 112 through 115 removed outlier: 4.357A pdb=" N GLN D 135 " --> pdb=" O MET D 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 120 through 122 Processing sheet with id=AD3, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.693A pdb=" N SER D 148 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL D 157 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 175 through 177 Processing sheet with id=AD5, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.781A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.284A pdb=" N GLU E 42 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.416A pdb=" N LEU E 66 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AD9, first strand: chain 'E' and resid 95 through 98 Processing sheet with id=AE1, first strand: chain 'E' and resid 103 through 106 Processing sheet with id=AE2, first strand: chain 'E' and resid 120 through 122 Processing sheet with id=AE3, first strand: chain 'E' and resid 148 through 151 removed outlier: 3.587A pdb=" N SER E 148 " --> pdb=" O THR E 160 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL E 157 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AE5, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.845A pdb=" N GLU E 185 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU E 191 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 37 through 43 removed outlier: 5.479A pdb=" N ARG F 38 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR F 77 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL F 40 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 46 through 50 removed outlier: 6.355A pdb=" N LEU F 66 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 88 removed outlier: 3.659A pdb=" N VAL F 219 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 95 through 98 Processing sheet with id=AF1, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.329A pdb=" N GLN F 135 " --> pdb=" O MET F 106 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 185 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 120 through 122 Processing sheet with id=AF3, first strand: chain 'F' and resid 148 through 151 removed outlier: 3.582A pdb=" N SER F 148 " --> pdb=" O THR F 160 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL F 157 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 175 through 177 removed outlier: 4.100A pdb=" N THR F 177 " --> pdb=" O ASN F 202 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN F 202 " --> pdb=" O THR F 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 37 through 43 removed outlier: 5.434A pdb=" N ARG G 38 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR G 77 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL G 40 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 46 through 50 removed outlier: 6.443A pdb=" N LEU G 66 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 86 through 88 removed outlier: 3.533A pdb=" N VAL G 219 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 95 through 98 Processing sheet with id=AF9, first strand: chain 'G' and resid 103 through 106 Processing sheet with id=AG1, first strand: chain 'G' and resid 121 through 122 Processing sheet with id=AG2, first strand: chain 'G' and resid 148 through 151 removed outlier: 3.992A pdb=" N SER G 148 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL G 157 " --> pdb=" O VAL G 170 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 175 through 177 Processing sheet with id=AG4, first strand: chain 'G' and resid 185 through 187 removed outlier: 3.501A pdb=" N GLU G 185 " --> pdb=" O ILE G 193 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 37 through 43 removed outlier: 6.096A pdb=" N ARG H 38 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR H 77 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL H 40 " --> pdb=" O VAL H 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 46 through 50 removed outlier: 6.416A pdb=" N LEU H 66 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 55 through 57 Processing sheet with id=AG8, first strand: chain 'H' and resid 86 through 88 Processing sheet with id=AG9, first strand: chain 'H' and resid 95 through 98 Processing sheet with id=AH1, first strand: chain 'H' and resid 135 through 136 removed outlier: 4.242A pdb=" N GLN H 135 " --> pdb=" O MET H 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 120 through 122 Processing sheet with id=AH3, first strand: chain 'H' and resid 148 through 151 removed outlier: 4.092A pdb=" N SER H 148 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL H 157 " --> pdb=" O VAL H 170 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 175 through 177 Processing sheet with id=AH5, first strand: chain 'I' and resid 37 through 43 removed outlier: 6.184A pdb=" N GLU I 42 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.338A pdb=" N LEU I 66 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 86 through 88 Processing sheet with id=AH8, first strand: chain 'I' and resid 95 through 98 Processing sheet with id=AH9, first strand: chain 'I' and resid 103 through 106 Processing sheet with id=AI1, first strand: chain 'I' and resid 120 through 122 Processing sheet with id=AI2, first strand: chain 'I' and resid 146 through 151 removed outlier: 7.217A pdb=" N VAL I 157 " --> pdb=" O VAL I 170 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 175 through 177 Processing sheet with id=AI4, first strand: chain 'I' and resid 185 through 187 removed outlier: 3.733A pdb=" N LEU I 191 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.273A pdb=" N ARG J 38 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR J 77 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL J 40 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 46 through 48 Processing sheet with id=AI7, first strand: chain 'J' and resid 86 through 88 Processing sheet with id=AI8, first strand: chain 'J' and resid 95 through 98 Processing sheet with id=AI9, first strand: chain 'J' and resid 112 through 115 removed outlier: 4.195A pdb=" N GLN J 135 " --> pdb=" O MET J 106 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 120 through 122 Processing sheet with id=AJ2, first strand: chain 'J' and resid 148 through 151 removed outlier: 3.801A pdb=" N SER J 148 " --> pdb=" O THR J 160 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL J 157 " --> pdb=" O VAL J 170 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AJ4, first strand: chain 'J' and resid 185 through 187 removed outlier: 3.885A pdb=" N LEU J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 37 through 43 removed outlier: 6.021A pdb=" N ARG K 38 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR K 77 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL K 40 " --> pdb=" O VAL K 75 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 46 through 48 Processing sheet with id=AJ7, first strand: chain 'K' and resid 86 through 88 Processing sheet with id=AJ8, first strand: chain 'K' and resid 95 through 98 Processing sheet with id=AJ9, first strand: chain 'K' and resid 135 through 136 removed outlier: 4.332A pdb=" N GLN K 135 " --> pdb=" O MET K 106 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'K' and resid 120 through 122 Processing sheet with id=AK2, first strand: chain 'K' and resid 148 through 151 removed outlier: 3.746A pdb=" N SER K 148 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL K 157 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'K' and resid 175 through 177 removed outlier: 3.736A pdb=" N THR K 177 " --> pdb=" O ASN K 202 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN K 202 " --> pdb=" O THR K 177 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 37 through 43 removed outlier: 6.622A pdb=" N ARG L 38 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR L 77 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL L 40 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.396A pdb=" N LEU L 66 " --> pdb=" O ILE L 49 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 86 through 88 Processing sheet with id=AK7, first strand: chain 'L' and resid 95 through 98 Processing sheet with id=AK8, first strand: chain 'L' and resid 112 through 115 removed outlier: 4.228A pdb=" N GLN L 135 " --> pdb=" O MET L 106 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'L' and resid 120 through 122 Processing sheet with id=AL1, first strand: chain 'L' and resid 148 through 151 removed outlier: 3.714A pdb=" N SER L 148 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL L 157 " --> pdb=" O VAL L 170 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 175 through 177 Processing sheet with id=AL3, first strand: chain 'L' and resid 185 through 187 removed outlier: 3.924A pdb=" N LEU L 191 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'M' and resid 37 through 43 removed outlier: 6.136A pdb=" N ARG M 38 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR M 77 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL M 40 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'M' and resid 46 through 48 Processing sheet with id=AL6, first strand: chain 'M' and resid 55 through 57 removed outlier: 3.666A pdb=" N THR M 60 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'M' and resid 86 through 88 Processing sheet with id=AL8, first strand: chain 'M' and resid 95 through 98 Processing sheet with id=AL9, first strand: chain 'M' and resid 112 through 115 removed outlier: 4.233A pdb=" N GLN M 135 " --> pdb=" O MET M 106 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 120 through 122 Processing sheet with id=AM2, first strand: chain 'M' and resid 148 through 151 removed outlier: 4.077A pdb=" N SER M 148 " --> pdb=" O THR M 160 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL M 157 " --> pdb=" O VAL M 170 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'M' and resid 175 through 177 Processing sheet with id=AM4, first strand: chain 'M' and resid 185 through 187 removed outlier: 3.863A pdb=" N LEU M 191 " --> pdb=" O ILE M 187 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 37 through 43 removed outlier: 3.612A pdb=" N ALA N 76 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU N 42 " --> pdb=" O PRO N 74 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'N' and resid 47 through 49 removed outlier: 4.830A pdb=" N LEU N 66 " --> pdb=" O ILE N 49 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'N' and resid 86 through 88 Processing sheet with id=AM8, first strand: chain 'N' and resid 95 through 98 Processing sheet with id=AM9, first strand: chain 'N' and resid 112 through 115 removed outlier: 4.143A pdb=" N GLN N 135 " --> pdb=" O MET N 106 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'N' and resid 120 through 122 Processing sheet with id=AN2, first strand: chain 'N' and resid 148 through 151 removed outlier: 3.820A pdb=" N SER N 148 " --> pdb=" O THR N 160 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL N 157 " --> pdb=" O VAL N 170 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'N' and resid 175 through 177 removed outlier: 3.537A pdb=" N LEU N 175 " --> pdb=" O SER N 204 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N 204 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR N 177 " --> pdb=" O ASN N 202 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN N 202 " --> pdb=" O THR N 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN3 Processing sheet with id=AN4, first strand: chain 'N' and resid 185 through 187 removed outlier: 3.761A pdb=" N LEU N 191 " --> pdb=" O ILE N 187 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'O' and resid 37 through 43 removed outlier: 3.505A pdb=" N ALA O 76 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU O 42 " --> pdb=" O PRO O 74 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'O' and resid 47 through 49 removed outlier: 4.504A pdb=" N LEU O 66 " --> pdb=" O ILE O 49 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'O' and resid 86 through 88 Processing sheet with id=AN8, first strand: chain 'O' and resid 95 through 98 Processing sheet with id=AN9, first strand: chain 'O' and resid 112 through 115 removed outlier: 4.049A pdb=" N GLN O 135 " --> pdb=" O MET O 106 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'O' and resid 120 through 122 Processing sheet with id=AO2, first strand: chain 'O' and resid 148 through 151 removed outlier: 3.660A pdb=" N SER O 148 " --> pdb=" O THR O 160 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL O 157 " --> pdb=" O VAL O 170 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'O' and resid 175 through 177 Processing sheet with id=AO4, first strand: chain 'O' and resid 185 through 187 removed outlier: 3.711A pdb=" N LEU O 191 " --> pdb=" O ILE O 187 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'P' and resid 37 through 43 removed outlier: 6.475A pdb=" N ARG P 38 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR P 77 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL P 40 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'P' and resid 47 through 49 removed outlier: 3.710A pdb=" N LEU P 66 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'P' and resid 86 through 88 Processing sheet with id=AO8, first strand: chain 'P' and resid 95 through 98 Processing sheet with id=AO9, first strand: chain 'P' and resid 112 through 115 removed outlier: 4.181A pdb=" N GLN P 135 " --> pdb=" O MET P 106 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'P' and resid 120 through 122 Processing sheet with id=AP2, first strand: chain 'P' and resid 149 through 151 removed outlier: 3.887A pdb=" N GLY P 171 " --> pdb=" O VAL P 157 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL P 159 " --> pdb=" O GLN P 169 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN P 169 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'P' and resid 175 through 177 Processing sheet with id=AP4, first strand: chain 'P' and resid 185 through 187 removed outlier: 3.884A pdb=" N LEU P 191 " --> pdb=" O ILE P 187 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'Q' and resid 37 through 43 removed outlier: 3.688A pdb=" N ALA Q 76 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLU Q 42 " --> pdb=" O PRO Q 74 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'Q' and resid 47 through 49 Processing sheet with id=AP7, first strand: chain 'Q' and resid 86 through 88 Processing sheet with id=AP8, first strand: chain 'Q' and resid 95 through 98 Processing sheet with id=AP9, first strand: chain 'Q' and resid 112 through 115 removed outlier: 3.952A pdb=" N GLN Q 135 " --> pdb=" O MET Q 106 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'Q' and resid 120 through 122 Processing sheet with id=AQ2, first strand: chain 'Q' and resid 148 through 151 removed outlier: 3.757A pdb=" N SER Q 148 " --> pdb=" O THR Q 160 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL Q 157 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'Q' and resid 175 through 177 Processing sheet with id=AQ4, first strand: chain 'Q' and resid 185 through 187 removed outlier: 3.737A pdb=" N LEU Q 191 " --> pdb=" O ILE Q 187 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'R' and resid 37 through 43 removed outlier: 3.667A pdb=" N ALA R 76 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU R 42 " --> pdb=" O PRO R 74 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'R' and resid 47 through 48 Processing sheet with id=AQ7, first strand: chain 'R' and resid 86 through 88 Processing sheet with id=AQ8, first strand: chain 'R' and resid 95 through 98 Processing sheet with id=AQ9, first strand: chain 'R' and resid 112 through 115 removed outlier: 3.974A pdb=" N GLN R 135 " --> pdb=" O MET R 106 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'R' and resid 120 through 122 Processing sheet with id=AR2, first strand: chain 'R' and resid 148 through 151 removed outlier: 3.540A pdb=" N SER R 148 " --> pdb=" O THR R 160 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL R 157 " --> pdb=" O VAL R 170 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'R' and resid 175 through 177 Processing sheet with id=AR4, first strand: chain 'R' and resid 185 through 187 removed outlier: 3.974A pdb=" N LEU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'S' and resid 37 through 43 removed outlier: 6.284A pdb=" N GLU S 42 " --> pdb=" O PRO S 74 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'S' and resid 47 through 49 removed outlier: 3.864A pdb=" N LEU S 66 " --> pdb=" O ILE S 49 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'S' and resid 86 through 88 Processing sheet with id=AR8, first strand: chain 'S' and resid 95 through 98 Processing sheet with id=AR9, first strand: chain 'S' and resid 112 through 115 removed outlier: 4.097A pdb=" N GLN S 135 " --> pdb=" O MET S 106 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'S' and resid 120 through 122 Processing sheet with id=AS2, first strand: chain 'S' and resid 149 through 151 removed outlier: 4.061A pdb=" N GLY S 171 " --> pdb=" O VAL S 157 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL S 159 " --> pdb=" O GLN S 169 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN S 169 " --> pdb=" O VAL S 159 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'S' and resid 175 through 177 Processing sheet with id=AS4, first strand: chain 'S' and resid 185 through 187 removed outlier: 3.609A pdb=" N LEU S 191 " --> pdb=" O ILE S 187 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'T' and resid 37 through 43 removed outlier: 3.525A pdb=" N ALA T 76 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU T 42 " --> pdb=" O PRO T 74 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'T' and resid 47 through 50 removed outlier: 3.836A pdb=" N ILE T 49 " --> pdb=" O LEU T 66 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU T 66 " --> pdb=" O ILE T 49 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'T' and resid 86 through 88 Processing sheet with id=AS8, first strand: chain 'T' and resid 95 through 98 Processing sheet with id=AS9, first strand: chain 'T' and resid 112 through 115 removed outlier: 4.232A pdb=" N GLN T 135 " --> pdb=" O MET T 106 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'T' and resid 120 through 122 Processing sheet with id=AT2, first strand: chain 'T' and resid 149 through 151 removed outlier: 6.317A pdb=" N VAL T 157 " --> pdb=" O VAL T 170 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'T' and resid 175 through 177 Processing sheet with id=AT4, first strand: chain 'U' and resid 37 through 43 removed outlier: 6.176A pdb=" N GLU U 42 " --> pdb=" O PRO U 74 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'U' and resid 47 through 50 removed outlier: 6.921A pdb=" N LEU U 66 " --> pdb=" O ILE U 49 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'U' and resid 86 through 88 Processing sheet with id=AT7, first strand: chain 'U' and resid 95 through 98 Processing sheet with id=AT8, first strand: chain 'U' and resid 103 through 106 Processing sheet with id=AT9, first strand: chain 'U' and resid 120 through 122 Processing sheet with id=AU1, first strand: chain 'U' and resid 149 through 151 removed outlier: 6.920A pdb=" N VAL U 157 " --> pdb=" O VAL U 170 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'U' and resid 175 through 177 Processing sheet with id=AU3, first strand: chain 'U' and resid 185 through 187 removed outlier: 3.627A pdb=" N LEU U 191 " --> pdb=" O ILE U 187 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'a' and resid 40 through 45 Processing sheet with id=AU5, first strand: chain 'a' and resid 71 through 73 Processing sheet with id=AU6, first strand: chain 'a' and resid 80 through 81 removed outlier: 3.620A pdb=" N MET a 202 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'a' and resid 97 through 100 Processing sheet with id=AU8, first strand: chain 'a' and resid 106 through 107 Processing sheet with id=AU9, first strand: chain 'a' and resid 134 through 137 removed outlier: 6.653A pdb=" N ILE a 143 " --> pdb=" O VAL a 158 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'a' and resid 171 through 173 Processing sheet with id=AV2, first strand: chain 'b' and resid 37 through 38 removed outlier: 3.574A pdb=" N LEU b 38 " --> pdb=" O GLY b 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY b 63 " --> pdb=" O LEU b 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV2 Processing sheet with id=AV3, first strand: chain 'b' and resid 42 through 45 Processing sheet with id=AV4, first strand: chain 'b' and resid 71 through 73 Processing sheet with id=AV5, first strand: chain 'b' and resid 80 through 81 removed outlier: 3.634A pdb=" N MET b 202 " --> pdb=" O ALA b 81 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'b' and resid 97 through 100 Processing sheet with id=AV7, first strand: chain 'b' and resid 106 through 107 Processing sheet with id=AV8, first strand: chain 'b' and resid 136 through 137 removed outlier: 6.481A pdb=" N ILE b 143 " --> pdb=" O VAL b 158 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'b' and resid 171 through 172 Processing sheet with id=AW1, first strand: chain 'c' and resid 40 through 45 Processing sheet with id=AW2, first strand: chain 'c' and resid 71 through 73 Processing sheet with id=AW3, first strand: chain 'c' and resid 80 through 81 removed outlier: 3.604A pdb=" N MET c 202 " --> pdb=" O ALA c 81 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'c' and resid 97 through 100 Processing sheet with id=AW5, first strand: chain 'c' and resid 106 through 107 Processing sheet with id=AW6, first strand: chain 'c' and resid 134 through 137 removed outlier: 3.561A pdb=" N GLY c 159 " --> pdb=" O ILE c 143 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA c 145 " --> pdb=" O PRO c 157 " (cutoff:3.500A) Processing sheet with id=AW7, first strand: chain 'c' and resid 171 through 172 Processing sheet with id=AW8, first strand: chain 'd' and resid 42 through 45 Processing sheet with id=AW9, first strand: chain 'd' and resid 71 through 73 Processing sheet with id=AX1, first strand: chain 'd' and resid 80 through 81 Processing sheet with id=AX2, first strand: chain 'd' and resid 97 through 100 Processing sheet with id=AX3, first strand: chain 'd' and resid 106 through 107 Processing sheet with id=AX4, first strand: chain 'd' and resid 134 through 137 removed outlier: 3.688A pdb=" N GLY d 159 " --> pdb=" O ILE d 143 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA d 145 " --> pdb=" O PRO d 157 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'd' and resid 171 through 173 Processing sheet with id=AX6, first strand: chain 'e' and resid 34 through 35 removed outlier: 7.831A pdb=" N PHE e 34 " --> pdb=" O ASN e 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX6 Processing sheet with id=AX7, first strand: chain 'e' and resid 40 through 45 Processing sheet with id=AX8, first strand: chain 'e' and resid 71 through 73 Processing sheet with id=AX9, first strand: chain 'e' and resid 80 through 81 Processing sheet with id=AY1, first strand: chain 'e' and resid 97 through 100 Processing sheet with id=AY2, first strand: chain 'e' and resid 106 through 107 Processing sheet with id=AY3, first strand: chain 'e' and resid 134 through 137 removed outlier: 6.690A pdb=" N ILE e 143 " --> pdb=" O VAL e 158 " (cutoff:3.500A) Processing sheet with id=AY4, first strand: chain 'e' and resid 171 through 173 Processing sheet with id=AY5, first strand: chain '5' and resid 316 through 317 Processing sheet with id=AY6, first strand: chain '7' and resid 316 through 317 Processing sheet with id=AY7, first strand: chain '9' and resid 316 through 317 Processing sheet with id=AY8, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.255A pdb=" N GLN f 46 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL f 67 " --> pdb=" O GLN f 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL f 48 " --> pdb=" O ALA f 65 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY f 61 " --> pdb=" O ASP f 52 " (cutoff:3.500A) Processing sheet with id=AY9, first strand: chain 'f' and resid 75 through 78 Processing sheet with id=AZ1, first strand: chain 'g' and resid 45 through 51 removed outlier: 4.237A pdb=" N VAL g 48 " --> pdb=" O SER g 66 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER g 66 " --> pdb=" O VAL g 48 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN g 50 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL g 64 " --> pdb=" O GLN g 50 " (cutoff:3.500A) Processing sheet with id=AZ2, first strand: chain 'g' and resid 75 through 78 Processing sheet with id=AZ3, first strand: chain 'h' and resid 45 through 51 removed outlier: 6.314A pdb=" N GLN h 46 " --> pdb=" O VAL h 67 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL h 67 " --> pdb=" O GLN h 46 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL h 48 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing sheet with id=AZ4, first strand: chain 'h' and resid 77 through 78 Processing sheet with id=AZ5, first strand: chain 'j' and resid 45 through 51 removed outlier: 4.042A pdb=" N SER j 66 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN j 50 " --> pdb=" O VAL j 64 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL j 64 " --> pdb=" O GLN j 50 " (cutoff:3.500A) Processing sheet with id=AZ6, first strand: chain 'j' and resid 76 through 78 Processing sheet with id=AZ7, first strand: chain 'l' and resid 41 through 42 Processing sheet with id=AZ8, first strand: chain 'p' and resid 45 through 51 removed outlier: 6.348A pdb=" N GLN p 46 " --> pdb=" O VAL p 67 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL p 67 " --> pdb=" O GLN p 46 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL p 48 " --> pdb=" O ALA p 65 " (cutoff:3.500A) Processing sheet with id=AZ9, first strand: chain 'p' and resid 75 through 78 Processing sheet with id=BA1, first strand: chain 'i' and resid 45 through 51 removed outlier: 6.230A pdb=" N GLN i 46 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL i 67 " --> pdb=" O GLN i 46 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL i 48 " --> pdb=" O ALA i 65 " (cutoff:3.500A) Processing sheet with id=BA2, first strand: chain 'i' and resid 76 through 78 Processing sheet with id=BA3, first strand: chain 'n' and resid 41 through 42 Processing sheet with id=BA4, first strand: chain 'V' and resid 37 through 43 removed outlier: 5.488A pdb=" N ARG V 38 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR V 77 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL V 40 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=BA5, first strand: chain 'V' and resid 47 through 50 removed outlier: 6.629A pdb=" N LEU V 66 " --> pdb=" O ILE V 49 " (cutoff:3.500A) Processing sheet with id=BA6, first strand: chain 'V' and resid 86 through 88 Processing sheet with id=BA7, first strand: chain 'V' and resid 95 through 98 Processing sheet with id=BA8, first strand: chain 'V' and resid 112 through 115 removed outlier: 4.413A pdb=" N GLN V 135 " --> pdb=" O MET V 106 " (cutoff:3.500A) Processing sheet with id=BA9, first strand: chain 'V' and resid 120 through 122 Processing sheet with id=BB1, first strand: chain 'V' and resid 148 through 151 removed outlier: 4.339A pdb=" N SER V 148 " --> pdb=" O THR V 160 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR V 160 " --> pdb=" O SER V 148 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL V 157 " --> pdb=" O VAL V 170 " (cutoff:3.500A) Processing sheet with id=BB2, first strand: chain 'V' and resid 175 through 177 Processing sheet with id=BB3, first strand: chain 'V' and resid 184 through 187 Processing sheet with id=BB4, first strand: chain 'W' and resid 37 through 43 removed outlier: 6.085A pdb=" N ARG W 38 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR W 77 " --> pdb=" O ARG W 38 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL W 40 " --> pdb=" O VAL W 75 " (cutoff:3.500A) Processing sheet with id=BB5, first strand: chain 'W' and resid 47 through 50 removed outlier: 6.863A pdb=" N LEU W 66 " --> pdb=" O ILE W 49 " (cutoff:3.500A) Processing sheet with id=BB6, first strand: chain 'W' and resid 86 through 88 Processing sheet with id=BB7, first strand: chain 'W' and resid 95 through 98 Processing sheet with id=BB8, first strand: chain 'W' and resid 112 through 115 removed outlier: 4.357A pdb=" N GLN W 135 " --> pdb=" O MET W 106 " (cutoff:3.500A) Processing sheet with id=BB9, first strand: chain 'W' and resid 120 through 122 Processing sheet with id=BC1, first strand: chain 'W' and resid 149 through 151 removed outlier: 7.097A pdb=" N VAL W 157 " --> pdb=" O VAL W 170 " (cutoff:3.500A) Processing sheet with id=BC2, first strand: chain 'W' and resid 175 through 177 Processing sheet with id=BC3, first strand: chain 'W' and resid 185 through 187 removed outlier: 3.990A pdb=" N LEU W 191 " --> pdb=" O ILE W 187 " (cutoff:3.500A) Processing sheet with id=BC4, first strand: chain 'X' and resid 37 through 43 removed outlier: 6.173A pdb=" N GLU X 42 " --> pdb=" O PRO X 74 " (cutoff:3.500A) Processing sheet with id=BC5, first strand: chain 'X' and resid 47 through 50 removed outlier: 6.857A pdb=" N LEU X 66 " --> pdb=" O ILE X 49 " (cutoff:3.500A) Processing sheet with id=BC6, first strand: chain 'X' and resid 86 through 88 Processing sheet with id=BC7, first strand: chain 'X' and resid 95 through 97 Processing sheet with id=BC8, first strand: chain 'X' and resid 112 through 115 removed outlier: 3.958A pdb=" N GLN X 135 " --> pdb=" O MET X 106 " (cutoff:3.500A) Processing sheet with id=BC9, first strand: chain 'X' and resid 120 through 122 Processing sheet with id=BD1, first strand: chain 'X' and resid 149 through 151 removed outlier: 6.848A pdb=" N VAL X 157 " --> pdb=" O VAL X 170 " (cutoff:3.500A) Processing sheet with id=BD2, first strand: chain 'X' and resid 175 through 177 Processing sheet with id=BD3, first strand: chain 'X' and resid 185 through 187 removed outlier: 3.962A pdb=" N LEU X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing sheet with id=BD4, first strand: chain 'DA' and resid 35 through 43 removed outlier: 3.962A pdb=" N SERDA 38 " --> pdb=" O GLYDA 56 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLYDA 56 " --> pdb=" O SERDA 38 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALADA 40 " --> pdb=" O VALDA 54 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VALDA 54 " --> pdb=" O ALADA 40 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N METDA 42 " --> pdb=" O VALDA 52 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VALDA 52 " --> pdb=" O METDA 42 " (cutoff:3.500A) Processing sheet with id=BD5, first strand: chain 'DA' and resid 66 through 67 Processing sheet with id=BD6, first strand: chain 'DA' and resid 75 through 77 Processing sheet with id=BD7, first strand: chain 'DA' and resid 135 through 136 removed outlier: 5.117A pdb=" N ARGDA 84 " --> pdb=" O THRDA 117 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N TYRDA 119 " --> pdb=" O PHEDA 82 " (cutoff:3.500A) removed outlier: 16.135A pdb=" N PHEDA 82 " --> pdb=" O TYRDA 119 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALADA 327 " --> pdb=" O ALADA 335 " (cutoff:3.500A) Processing sheet with id=BD8, first strand: chain 'DA' and resid 291 through 294 removed outlier: 3.772A pdb=" N SERDA 291 " --> pdb=" O ASNDA 303 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VALDA 300 " --> pdb=" O LEUDA 312 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLNDA 310 " --> pdb=" O GLYDA 302 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLNDA 314 " --> pdb=" O TYRDA 119 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARGDA 84 " --> pdb=" O THRDA 117 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N TYRDA 119 " --> pdb=" O PHEDA 82 " (cutoff:3.500A) removed outlier: 16.135A pdb=" N PHEDA 82 " --> pdb=" O TYRDA 119 " (cutoff:3.500A) Processing sheet with id=BD9, first strand: chain 'DA' and resid 100 through 101 Processing sheet with id=BE1, first strand: chain 'DA' and resid 121 through 122 Processing sheet with id=BE2, first strand: chain 'DA' and resid 243 through 247 removed outlier: 7.117A pdb=" N SERDA 153 " --> pdb=" O THRDA 279 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THRDA 279 " --> pdb=" O SERDA 153 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLNDA 155 " --> pdb=" O VALDA 277 " (cutoff:3.500A) Processing sheet with id=BE3, first strand: chain 'DA' and resid 180 through 187 removed outlier: 3.651A pdb=" N THRDA 203 " --> pdb=" O GLUDA 207 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLUDA 207 " --> pdb=" O THRDA 203 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N LYSDA 231 " --> pdb=" O GLUDA 239 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLUDA 239 " --> pdb=" O LYSDA 231 " (cutoff:3.500A) Processing sheet with id=BE4, first strand: chain 'DB' and resid 35 through 36 Processing sheet with id=BE5, first strand: chain 'DB' and resid 39 through 43 removed outlier: 6.771A pdb=" N ALADB 40 " --> pdb=" O VALDB 52 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VALDB 52 " --> pdb=" O ALADB 40 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N METDB 42 " --> pdb=" O LEUDB 50 " (cutoff:3.500A) Processing sheet with id=BE6, first strand: chain 'DB' and resid 66 through 67 Processing sheet with id=BE7, first strand: chain 'DB' and resid 75 through 77 Processing sheet with id=BE8, first strand: chain 'DB' and resid 135 through 136 removed outlier: 5.406A pdb=" N ARGDB 84 " --> pdb=" O THRDB 117 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N TYRDB 119 " --> pdb=" O PHEDB 82 " (cutoff:3.500A) removed outlier: 16.335A pdb=" N PHEDB 82 " --> pdb=" O TYRDB 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALADB 327 " --> pdb=" O ALADB 335 " (cutoff:3.500A) Processing sheet with id=BE9, first strand: chain 'DB' and resid 289 through 294 removed outlier: 3.861A pdb=" N SERDB 291 " --> pdb=" O ASNDB 303 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLYDB 313 " --> pdb=" O VALDB 300 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLYDB 302 " --> pdb=" O VALDB 311 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VALDB 311 " --> pdb=" O GLYDB 302 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARGDB 84 " --> pdb=" O THRDB 117 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N TYRDB 119 " --> pdb=" O PHEDB 82 " (cutoff:3.500A) removed outlier: 16.335A pdb=" N PHEDB 82 " --> pdb=" O TYRDB 119 " (cutoff:3.500A) Processing sheet with id=BF1, first strand: chain 'DB' and resid 100 through 102 Processing sheet with id=BF2, first strand: chain 'DB' and resid 121 through 122 Processing sheet with id=BF3, first strand: chain 'DB' and resid 243 through 247 removed outlier: 6.952A pdb=" N ALADB 152 " --> pdb=" O SERDB 262 " (cutoff:3.500A) Processing sheet with id=BF4, first strand: chain 'DB' and resid 180 through 187 Processing sheet with id=BF5, first strand: chain 'DC' and resid 35 through 41 removed outlier: 3.851A pdb=" N GLYDC 56 " --> pdb=" O SERDC 38 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALADC 40 " --> pdb=" O VALDC 54 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VALDC 54 " --> pdb=" O ALADC 40 " (cutoff:3.500A) Processing sheet with id=BF6, first strand: chain 'DC' and resid 75 through 77 Processing sheet with id=BF7, first strand: chain 'DC' and resid 92 through 95 removed outlier: 16.710A pdb=" N PHEDC 82 " --> pdb=" O TYRDC 119 " (cutoff:3.500A) removed outlier: 11.574A pdb=" N TYRDC 119 " --> pdb=" O PHEDC 82 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARGDC 84 " --> pdb=" O THRDC 117 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLNDC 314 " --> pdb=" O TYRDC 119 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VALDC 300 " --> pdb=" O LEUDC 312 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THRDC 299 " --> pdb=" O ILEDC 294 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILEDC 294 " --> pdb=" O THRDC 299 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VALDC 301 " --> pdb=" O TYRDC 292 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYRDC 292 " --> pdb=" O VALDC 301 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASNDC 303 " --> pdb=" O VALDC 290 " (cutoff:3.500A) Processing sheet with id=BF8, first strand: chain 'DC' and resid 135 through 136 removed outlier: 5.478A pdb=" N ARGDC 84 " --> pdb=" O THRDC 117 " (cutoff:3.500A) removed outlier: 11.574A pdb=" N TYRDC 119 " --> pdb=" O PHEDC 82 " (cutoff:3.500A) removed outlier: 16.710A pdb=" N PHEDC 82 " --> pdb=" O TYRDC 119 " (cutoff:3.500A) Processing sheet with id=BF9, first strand: chain 'DC' and resid 100 through 102 Processing sheet with id=BG1, first strand: chain 'DC' and resid 121 through 122 Processing sheet with id=BG2, first strand: chain 'DC' and resid 243 through 247 removed outlier: 7.233A pdb=" N THRDC 151 " --> pdb=" O GLNDC 281 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLNDC 281 " --> pdb=" O THRDC 151 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SERDC 153 " --> pdb=" O THRDC 279 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THRDC 279 " --> pdb=" O SERDC 153 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLNDC 155 " --> pdb=" O VALDC 277 " (cutoff:3.500A) Processing sheet with id=BG3, first strand: chain 'DC' and resid 180 through 187 removed outlier: 3.900A pdb=" N THRDC 203 " --> pdb=" O GLUDC 207 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLUDC 207 " --> pdb=" O THRDC 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THRDC 228 " --> pdb=" O VALDC 210 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYSDC 231 " --> pdb=" O GLUDC 239 " (cutoff:3.500A) Processing sheet with id=BG4, first strand: chain 'DC' and resid 327 through 328 Processing sheet with id=BG5, first strand: chain 'DD' and resid 35 through 43 removed outlier: 3.659A pdb=" N GLYDD 56 " --> pdb=" O SERDD 38 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALADD 40 " --> pdb=" O VALDD 54 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VALDD 54 " --> pdb=" O ALADD 40 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N METDD 42 " --> pdb=" O VALDD 52 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VALDD 52 " --> pdb=" O METDD 42 " (cutoff:3.500A) Processing sheet with id=BG6, first strand: chain 'DD' and resid 66 through 67 Processing sheet with id=BG7, first strand: chain 'DD' and resid 75 through 77 Processing sheet with id=BG8, first strand: chain 'DD' and resid 327 through 328 removed outlier: 3.625A pdb=" N ALADD 327 " --> pdb=" O ALADD 335 " (cutoff:3.500A) Processing sheet with id=BG9, first strand: chain 'DD' and resid 345 through 346 removed outlier: 16.279A pdb=" N PHEDD 82 " --> pdb=" O TYRDD 119 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N TYRDD 119 " --> pdb=" O PHEDD 82 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARGDD 84 " --> pdb=" O THRDD 117 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALADD 121 " --> pdb=" O LEUDD 312 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEUDD 312 " --> pdb=" O ALADD 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLNDD 310 " --> pdb=" O GLYDD 302 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VALDD 300 " --> pdb=" O LEUDD 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERDD 291 " --> pdb=" O ASNDD 303 " (cutoff:3.500A) Processing sheet with id=BH1, first strand: chain 'DD' and resid 291 through 294 removed outlier: 3.554A pdb=" N SERDD 291 " --> pdb=" O ASNDD 303 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VALDD 300 " --> pdb=" O LEUDD 312 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLNDD 310 " --> pdb=" O GLYDD 302 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEUDD 312 " --> pdb=" O ALADD 121 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALADD 121 " --> pdb=" O LEUDD 312 " (cutoff:3.500A) Processing sheet with id=BH2, first strand: chain 'DD' and resid 135 through 136 Processing sheet with id=BH3, first strand: chain 'DD' and resid 100 through 102 Processing sheet with id=BH4, first strand: chain 'DD' and resid 152 through 157 removed outlier: 3.735A pdb=" N SERDD 153 " --> pdb=" O ASNDD 280 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASNDD 280 " --> pdb=" O SERDD 153 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLNDD 155 " --> pdb=" O ALADD 278 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALADD 278 " --> pdb=" O GLNDD 155 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASNDD 157 " --> pdb=" O ILEDD 276 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILEDD 276 " --> pdb=" O ASNDD 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=BH4 Processing sheet with id=BH5, first strand: chain 'DD' and resid 180 through 187 removed outlier: 4.091A pdb=" N THRDD 203 " --> pdb=" O GLUDD 207 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLUDD 207 " --> pdb=" O THRDD 203 " (cutoff:3.500A) Processing sheet with id=BH6, first strand: chain 'DD' and resid 243 through 248 removed outlier: 4.369A pdb=" N ALADD 257 " --> pdb=" O THRDD 248 " (cutoff:3.500A) Processing sheet with id=BH7, first strand: chain 'DE' and resid 35 through 36 Processing sheet with id=BH8, first strand: chain 'DE' and resid 39 through 43 removed outlier: 3.966A pdb=" N GLYDE 51 " --> pdb=" O METDE 42 " (cutoff:3.500A) Processing sheet with id=BH9, first strand: chain 'DE' and resid 66 through 67 Processing sheet with id=BI1, first strand: chain 'DE' and resid 75 through 77 Processing sheet with id=BI2, first strand: chain 'DE' and resid 92 through 95 removed outlier: 3.777A pdb=" N ARGDE 84 " --> pdb=" O VALDE 316 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VALDE 316 " --> pdb=" O ARGDE 84 " (cutoff:3.500A) Processing sheet with id=BI3, first strand: chain 'DE' and resid 345 through 347 removed outlier: 6.583A pdb=" N VALDE 316 " --> pdb=" O ARGDE 84 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARGDE 84 " --> pdb=" O VALDE 316 " (cutoff:3.500A) removed outlier: 16.320A pdb=" N PHEDE 82 " --> pdb=" O TYRDE 119 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N TYRDE 119 " --> pdb=" O PHEDE 82 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARGDE 84 " --> pdb=" O THRDE 117 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALADE 121 " --> pdb=" O LEUDE 312 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEUDE 312 " --> pdb=" O ALADE 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLNDE 308 " --> pdb=" O TYRDE 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VALDE 300 " --> pdb=" O LEUDE 312 " (cutoff:3.500A) Processing sheet with id=BI4, first strand: chain 'DE' and resid 289 through 294 removed outlier: 6.461A pdb=" N VALDE 300 " --> pdb=" O LEUDE 312 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLNDE 308 " --> pdb=" O TYRDE 304 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEUDE 312 " --> pdb=" O ALADE 121 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALADE 121 " --> pdb=" O LEUDE 312 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THRDE 122 " --> pdb=" O THRDE 127 " (cutoff:3.500A) Processing sheet with id=BI5, first strand: chain 'DE' and resid 135 through 136 removed outlier: 3.670A pdb=" N THRDE 122 " --> pdb=" O THRDE 127 " (cutoff:3.500A) Processing sheet with id=BI6, first strand: chain 'DE' and resid 101 through 102 Processing sheet with id=BI7, first strand: chain 'DE' and resid 243 through 248 removed outlier: 4.532A pdb=" N ALADE 257 " --> pdb=" O THRDE 248 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THRDE 151 " --> pdb=" O GLNDE 281 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLNDE 281 " --> pdb=" O THRDE 151 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SERDE 153 " --> pdb=" O THRDE 279 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THRDE 279 " --> pdb=" O SERDE 153 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLNDE 155 " --> pdb=" O VALDE 277 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASNDE 275 " --> pdb=" O ASNDE 157 " (cutoff:3.500A) Processing sheet with id=BI8, first strand: chain 'DE' and resid 180 through 187 removed outlier: 3.882A pdb=" N LYSDE 180 " --> pdb=" O PHEDE 200 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLUDE 207 " --> pdb=" O THRDE 203 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LYSDE 231 " --> pdb=" O GLUDE 239 " (cutoff:3.500A) Processing sheet with id=BI9, first strand: chain 'DE' and resid 327 through 328 removed outlier: 3.809A pdb=" N ALADE 327 " --> pdb=" O ALADE 335 " (cutoff:3.500A) Processing sheet with id=BJ1, first strand: chain 'DF' and resid 35 through 36 Processing sheet with id=BJ2, first strand: chain 'DF' and resid 39 through 41 Processing sheet with id=BJ3, first strand: chain 'DF' and resid 66 through 67 Processing sheet with id=BJ4, first strand: chain 'DF' and resid 115 through 116 removed outlier: 3.528A pdb=" N ALADF 327 " --> pdb=" O ALADF 335 " (cutoff:3.500A) Processing sheet with id=BJ5, first strand: chain 'DF' and resid 115 through 116 removed outlier: 3.715A pdb=" N LEUDF 317 " --> pdb=" O GLYDF 346 " (cutoff:3.500A) Processing sheet with id=BJ6, first strand: chain 'DF' and resid 101 through 102 Processing sheet with id=BJ7, first strand: chain 'DF' and resid 121 through 122 Processing sheet with id=BJ8, first strand: chain 'DF' and resid 243 through 247 removed outlier: 3.786A pdb=" N SERDF 153 " --> pdb=" O ASNDF 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASNDF 280 " --> pdb=" O SERDF 153 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLNDF 155 " --> pdb=" O ALADF 278 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALADF 278 " --> pdb=" O GLNDF 155 " (cutoff:3.500A) Processing sheet with id=BJ9, first strand: chain 'DF' and resid 180 through 187 removed outlier: 3.753A pdb=" N THRDF 203 " --> pdb=" O GLUDF 207 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLUDF 207 " --> pdb=" O THRDF 203 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THRDF 228 " --> pdb=" O VALDF 210 " (cutoff:3.500A) Processing sheet with id=BK1, first strand: chain 'DF' and resid 289 through 294 removed outlier: 3.974A pdb=" N SERDF 291 " --> pdb=" O ASNDF 303 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLYDF 313 " --> pdb=" O VALDF 300 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLYDF 302 " --> pdb=" O VALDF 311 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VALDF 311 " --> pdb=" O GLYDF 302 " (cutoff:3.500A) Processing sheet with id=BK2, first strand: chain 'DG' and resid 35 through 36 Processing sheet with id=BK3, first strand: chain 'DG' and resid 39 through 41 Processing sheet with id=BK4, first strand: chain 'DG' and resid 66 through 67 Processing sheet with id=BK5, first strand: chain 'DG' and resid 75 through 77 Processing sheet with id=BK6, first strand: chain 'DG' and resid 92 through 95 removed outlier: 5.789A pdb=" N ARGDG 84 " --> pdb=" O THRDG 117 " (cutoff:3.500A) Processing sheet with id=BK7, first strand: chain 'DG' and resid 92 through 95 Processing sheet with id=BK8, first strand: chain 'DG' and resid 100 through 101 Processing sheet with id=BK9, first strand: chain 'DG' and resid 121 through 122 Processing sheet with id=BL1, first strand: chain 'DG' and resid 243 through 247 removed outlier: 3.556A pdb=" N PHEDG 259 " --> pdb=" O ILEDG 246 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SERDG 153 " --> pdb=" O ASNDG 280 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASNDG 280 " --> pdb=" O SERDG 153 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALADG 278 " --> pdb=" O GLNDG 155 " (cutoff:3.500A) Processing sheet with id=BL2, first strand: chain 'DG' and resid 180 through 187 Processing sheet with id=BL3, first strand: chain 'DG' and resid 289 through 294 removed outlier: 3.662A pdb=" N SERDG 291 " --> pdb=" O ASNDG 303 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASNDG 303 " --> pdb=" O SERDG 291 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VALDG 300 " --> pdb=" O LEUDG 312 " (cutoff:3.500A) Processing sheet with id=BL4, first strand: chain 'DG' and resid 327 through 329 removed outlier: 3.573A pdb=" N ALADG 327 " --> pdb=" O ALADG 335 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VALDG 333 " --> pdb=" O GLNDG 329 " (cutoff:3.500A) Processing sheet with id=BL5, first strand: chain 'DH' and resid 35 through 36 Processing sheet with id=BL6, first strand: chain 'DH' and resid 39 through 41 Processing sheet with id=BL7, first strand: chain 'DH' and resid 75 through 77 Processing sheet with id=BL8, first strand: chain 'DH' and resid 135 through 136 removed outlier: 3.542A pdb=" N GLNDH 314 " --> pdb=" O TYRDH 119 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLUDH 309 " --> pdb=" O TYRDH 304 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYRDH 304 " --> pdb=" O GLUDH 309 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VALDH 311 " --> pdb=" O GLYDH 302 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLYDH 302 " --> pdb=" O VALDH 311 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLYDH 313 " --> pdb=" O VALDH 300 " (cutoff:3.500A) Processing sheet with id=BL9, first strand: chain 'DH' and resid 135 through 136 removed outlier: 5.183A pdb=" N ARGDH 84 " --> pdb=" O THRDH 117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VALDH 333 " --> pdb=" O GLNDH 329 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALADH 327 " --> pdb=" O ALADH 335 " (cutoff:3.500A) Processing sheet with id=BM1, first strand: chain 'DH' and resid 100 through 102 Processing sheet with id=BM2, first strand: chain 'DH' and resid 121 through 122 Processing sheet with id=BM3, first strand: chain 'DH' and resid 243 through 247 removed outlier: 3.578A pdb=" N ILEDH 246 " --> pdb=" O PHEDH 259 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHEDH 259 " --> pdb=" O ILEDH 246 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALADH 152 " --> pdb=" O SERDH 260 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASNDH 157 " --> pdb=" O ILEDH 276 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILEDH 276 " --> pdb=" O ASNDH 157 " (cutoff:3.500A) Processing sheet with id=BM4, first strand: chain 'DH' and resid 180 through 182 Processing sheet with id=BM5, first strand: chain 'DH' and resid 180 through 182 removed outlier: 8.786A pdb=" N LYSDH 231 " --> pdb=" O GLUDH 239 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLUDH 239 " --> pdb=" O LYSDH 231 " (cutoff:3.500A) Processing sheet with id=BM6, first strand: chain 'DH' and resid 317 through 318 Processing sheet with id=BM7, first strand: chain 'DI' and resid 35 through 41 removed outlier: 3.641A pdb=" N SERDI 38 " --> pdb=" O GLYDI 56 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLYDI 56 " --> pdb=" O SERDI 38 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALADI 40 " --> pdb=" O VALDI 54 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VALDI 54 " --> pdb=" O ALADI 40 " (cutoff:3.500A) Processing sheet with id=BM8, first strand: chain 'DI' and resid 66 through 67 Processing sheet with id=BM9, first strand: chain 'DI' and resid 75 through 77 Processing sheet with id=BN1, first strand: chain 'DI' and resid 92 through 95 removed outlier: 16.024A pdb=" N PHEDI 82 " --> pdb=" O TYRDI 119 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N TYRDI 119 " --> pdb=" O PHEDI 82 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARGDI 84 " --> pdb=" O THRDI 117 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VALDI 300 " --> pdb=" O LEUDI 312 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SERDI 291 " --> pdb=" O ASNDI 303 " (cutoff:3.500A) Processing sheet with id=BN2, first strand: chain 'DI' and resid 135 through 136 removed outlier: 4.913A pdb=" N ARGDI 84 " --> pdb=" O THRDI 117 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N TYRDI 119 " --> pdb=" O PHEDI 82 " (cutoff:3.500A) removed outlier: 16.024A pdb=" N PHEDI 82 " --> pdb=" O TYRDI 119 " (cutoff:3.500A) Processing sheet with id=BN3, first strand: chain 'DI' and resid 101 through 102 Processing sheet with id=BN4, first strand: chain 'DI' and resid 121 through 122 Processing sheet with id=BN5, first strand: chain 'DI' and resid 243 through 247 removed outlier: 3.515A pdb=" N PHEDI 259 " --> pdb=" O ILEDI 246 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THRDI 151 " --> pdb=" O GLNDI 281 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLNDI 281 " --> pdb=" O THRDI 151 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SERDI 153 " --> pdb=" O THRDI 279 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THRDI 279 " --> pdb=" O SERDI 153 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLNDI 155 " --> pdb=" O VALDI 277 " (cutoff:3.500A) Processing sheet with id=BN6, first strand: chain 'DI' and resid 180 through 187 removed outlier: 3.572A pdb=" N LYSDI 180 " --> pdb=" O PHEDI 200 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLUDI 207 " --> pdb=" O THRDI 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALDI 210 " --> pdb=" O THRDI 228 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THRDI 228 " --> pdb=" O VALDI 210 " (cutoff:3.500A) Processing sheet with id=BN7, first strand: chain 'DI' and resid 327 through 328 removed outlier: 3.699A pdb=" N ALADI 327 " --> pdb=" O ALADI 335 " (cutoff:3.500A) Processing sheet with id=BN8, first strand: chain 'DJ' and resid 35 through 41 removed outlier: 6.291A pdb=" N THRDJ 36 " --> pdb=" O ILEDJ 57 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILEDJ 57 " --> pdb=" O THRDJ 36 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SERDJ 38 " --> pdb=" O ALADJ 55 " (cutoff:3.500A) Processing sheet with id=BN9, first strand: chain 'DJ' and resid 66 through 67 Processing sheet with id=BO1, first strand: chain 'DJ' and resid 75 through 77 Processing sheet with id=BO2, first strand: chain 'DJ' and resid 92 through 95 removed outlier: 5.447A pdb=" N ARGDJ 84 " --> pdb=" O THRDJ 117 " (cutoff:3.500A) Processing sheet with id=BO3, first strand: chain 'DJ' and resid 92 through 95 removed outlier: 3.970A pdb=" N ARGDJ 84 " --> pdb=" O VALDJ 316 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VALDJ 316 " --> pdb=" O ARGDJ 84 " (cutoff:3.500A) Processing sheet with id=BO4, first strand: chain 'DJ' and resid 101 through 102 Processing sheet with id=BO5, first strand: chain 'DJ' and resid 121 through 122 removed outlier: 3.610A pdb=" N THRDJ 122 " --> pdb=" O THRDJ 127 " (cutoff:3.500A) Processing sheet with id=BO6, first strand: chain 'DJ' and resid 243 through 247 removed outlier: 7.694A pdb=" N SERDJ 153 " --> pdb=" O THRDJ 279 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THRDJ 279 " --> pdb=" O SERDJ 153 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLNDJ 155 " --> pdb=" O VALDJ 277 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASNDJ 275 " --> pdb=" O ASNDJ 157 " (cutoff:3.500A) Processing sheet with id=BO7, first strand: chain 'DJ' and resid 180 through 187 removed outlier: 3.907A pdb=" N THRDJ 203 " --> pdb=" O GLUDJ 207 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLUDJ 207 " --> pdb=" O THRDJ 203 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYSDJ 231 " --> pdb=" O GLUDJ 239 " (cutoff:3.500A) Processing sheet with id=BO8, first strand: chain 'DJ' and resid 289 through 294 removed outlier: 6.218A pdb=" N VALDJ 300 " --> pdb=" O LEUDJ 312 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLYDJ 302 " --> pdb=" O GLNDJ 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLNDJ 310 " --> pdb=" O GLYDJ 302 " (cutoff:3.500A) Processing sheet with id=BO9, first strand: chain 'DJ' and resid 327 through 328 removed outlier: 3.536A pdb=" N ALADJ 327 " --> pdb=" O ALADJ 335 " (cutoff:3.500A) Processing sheet with id=BP1, first strand: chain 'DK' and resid 39 through 41 Processing sheet with id=BP2, first strand: chain 'DK' and resid 66 through 68 Processing sheet with id=BP3, first strand: chain 'DK' and resid 75 through 77 Processing sheet with id=BP4, first strand: chain 'DK' and resid 92 through 95 removed outlier: 3.697A pdb=" N PHEDK 82 " --> pdb=" O ALADK 318 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALADK 318 " --> pdb=" O PHEDK 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARGDK 84 " --> pdb=" O VALDK 316 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VALDK 316 " --> pdb=" O ARGDK 84 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N VALDK 86 " --> pdb=" O GLNDK 314 " (cutoff:3.500A) removed outlier: 15.975A pdb=" N GLNDK 314 " --> pdb=" O VALDK 86 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLUDK 309 " --> pdb=" O TYRDK 304 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYRDK 304 " --> pdb=" O GLUDK 309 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VALDK 311 " --> pdb=" O GLYDK 302 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLYDK 302 " --> pdb=" O VALDK 311 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYDK 313 " --> pdb=" O VALDK 300 " (cutoff:3.500A) Processing sheet with id=BP5, first strand: chain 'DK' and resid 345 through 347 removed outlier: 7.326A pdb=" N GLUDK 309 " --> pdb=" O TYRDK 304 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYRDK 304 " --> pdb=" O GLUDK 309 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VALDK 311 " --> pdb=" O GLYDK 302 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLYDK 302 " --> pdb=" O VALDK 311 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYDK 313 " --> pdb=" O VALDK 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERDK 291 " --> pdb=" O ASNDK 303 " (cutoff:3.500A) Processing sheet with id=BP6, first strand: chain 'DK' and resid 289 through 294 removed outlier: 3.515A pdb=" N SERDK 291 " --> pdb=" O ASNDK 303 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYDK 313 " --> pdb=" O VALDK 300 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLYDK 302 " --> pdb=" O VALDK 311 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VALDK 311 " --> pdb=" O GLYDK 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYRDK 304 " --> pdb=" O GLUDK 309 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLUDK 309 " --> pdb=" O TYRDK 304 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEUDK 312 " --> pdb=" O ALADK 121 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALADK 121 " --> pdb=" O LEUDK 312 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLNDK 314 " --> pdb=" O TYRDK 119 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VALDK 316 " --> pdb=" O THRDK 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THRDK 117 " --> pdb=" O VALDK 316 " (cutoff:3.500A) removed outlier: 12.617A pdb=" N ALADK 318 " --> pdb=" O GLNDK 115 " (cutoff:3.500A) removed outlier: 15.964A pdb=" N GLNDK 115 " --> pdb=" O ALADK 318 " (cutoff:3.500A) Processing sheet with id=BP7, first strand: chain 'DK' and resid 92 through 95 removed outlier: 16.538A pdb=" N PHEDK 82 " --> pdb=" O TYRDK 119 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N TYRDK 119 " --> pdb=" O PHEDK 82 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARGDK 84 " --> pdb=" O THRDK 117 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THRDK 117 " --> pdb=" O ARGDK 84 " (cutoff:3.500A) Processing sheet with id=BP8, first strand: chain 'DK' and resid 101 through 102 Processing sheet with id=BP9, first strand: chain 'DK' and resid 243 through 247 removed outlier: 3.945A pdb=" N PHEDK 259 " --> pdb=" O ILEDK 246 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALADK 278 " --> pdb=" O GLNDK 155 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASNDK 157 " --> pdb=" O ILEDK 276 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILEDK 276 " --> pdb=" O ASNDK 157 " (cutoff:3.500A) Processing sheet with id=BQ1, first strand: chain 'DK' and resid 180 through 187 removed outlier: 7.082A pdb=" N GLUDK 207 " --> pdb=" O THRDK 203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THRDK 228 " --> pdb=" O VALDK 210 " (cutoff:3.500A) Processing sheet with id=BQ2, first strand: chain 'DK' and resid 327 through 329 removed outlier: 3.617A pdb=" N ALADK 327 " --> pdb=" O ALADK 335 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VALDK 333 " --> pdb=" O GLNDK 329 " (cutoff:3.500A) 4535 hydrogen bonds defined for protein. 12654 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: 62.79 Time building geometry restraints manager: 33.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 18269 1.30 - 1.43: 23532 1.43 - 1.55: 60404 1.55 - 1.68: 0 1.68 - 1.81: 704 Bond restraints: 102909 Sorted by residual: bond pdb=" CA SERDJ 350 " pdb=" CB SERDJ 350 " ideal model delta sigma weight residual 1.538 1.482 0.057 1.22e-02 6.72e+03 2.15e+01 bond pdb=" C TYRDK 382 " pdb=" O TYRDK 382 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.29e-02 6.01e+03 2.06e+01 bond pdb=" CA SERDJ 384 " pdb=" CB SERDJ 384 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.58e-02 4.01e+03 1.10e+01 bond pdb=" C VAL W 170 " pdb=" O VAL W 170 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N SER 7 317 " pdb=" CA SER 7 317 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.10e+00 ... (remaining 102904 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.58: 2511 106.58 - 114.00: 59816 114.00 - 121.43: 50218 121.43 - 128.85: 27210 128.85 - 136.28: 183 Bond angle restraints: 139938 Sorted by residual: angle pdb=" C GLNDJ 383 " pdb=" CA GLNDJ 383 " pdb=" CB GLNDJ 383 " ideal model delta sigma weight residual 110.88 99.15 11.73 1.57e+00 4.06e-01 5.58e+01 angle pdb=" C ASNDI 270 " pdb=" N THRDI 271 " pdb=" CA THRDI 271 " ideal model delta sigma weight residual 122.27 110.45 11.82 1.85e+00 2.92e-01 4.08e+01 angle pdb=" N ASNDJ 381 " pdb=" CA ASNDJ 381 " pdb=" C ASNDJ 381 " ideal model delta sigma weight residual 111.28 104.94 6.34 1.09e+00 8.42e-01 3.39e+01 angle pdb=" C GLUDK 104 " pdb=" CA GLUDK 104 " pdb=" CB GLUDK 104 " ideal model delta sigma weight residual 110.67 121.16 -10.49 1.92e+00 2.71e-01 2.99e+01 angle pdb=" C TYRDJ 382 " pdb=" CA TYRDJ 382 " pdb=" CB TYRDJ 382 " ideal model delta sigma weight residual 110.79 103.70 7.09 1.66e+00 3.63e-01 1.83e+01 ... (remaining 139933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 59180 17.97 - 35.94: 2376 35.94 - 53.92: 379 53.92 - 71.89: 56 71.89 - 89.86: 51 Dihedral angle restraints: 62042 sinusoidal: 23218 harmonic: 38824 Sorted by residual: dihedral pdb=" C GLNDJ 383 " pdb=" N GLNDJ 383 " pdb=" CA GLNDJ 383 " pdb=" CB GLNDJ 383 " ideal model delta harmonic sigma weight residual -122.60 -107.17 -15.43 0 2.50e+00 1.60e-01 3.81e+01 dihedral pdb=" C GLUDK 104 " pdb=" N GLUDK 104 " pdb=" CA GLUDK 104 " pdb=" CB GLUDK 104 " ideal model delta harmonic sigma weight residual -122.60 -136.43 13.83 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" C ASPDJ 331 " pdb=" N ASPDJ 331 " pdb=" CA ASPDJ 331 " pdb=" CB ASPDJ 331 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.60e+01 ... (remaining 62039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 15407 0.085 - 0.169: 1103 0.169 - 0.254: 5 0.254 - 0.338: 1 0.338 - 0.423: 4 Chirality restraints: 16520 Sorted by residual: chirality pdb=" CA GLNDJ 383 " pdb=" N GLNDJ 383 " pdb=" C GLNDJ 383 " pdb=" CB GLNDJ 383 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA ASPDJ 331 " pdb=" N ASPDJ 331 " pdb=" C ASPDJ 331 " pdb=" CB ASPDJ 331 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA GLUDK 104 " pdb=" N GLUDK 104 " pdb=" C GLUDK 104 " pdb=" CB GLUDK 104 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 16517 not shown) Planarity restraints: 18779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYRDK 382 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C TYRDK 382 " 0.061 2.00e-02 2.50e+03 pdb=" O TYRDK 382 " -0.023 2.00e-02 2.50e+03 pdb=" N GLNDK 383 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYDJ 349 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C GLYDJ 349 " 0.048 2.00e-02 2.50e+03 pdb=" O GLYDJ 349 " -0.018 2.00e-02 2.50e+03 pdb=" N SERDJ 350 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLNDI 268 " 0.011 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C GLNDI 268 " -0.042 2.00e-02 2.50e+03 pdb=" O GLNDI 268 " 0.017 2.00e-02 2.50e+03 pdb=" N GLNDI 269 " 0.014 2.00e-02 2.50e+03 ... (remaining 18776 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1438 2.63 - 3.20: 95283 3.20 - 3.76: 152997 3.76 - 4.33: 201914 4.33 - 4.90: 345248 Nonbonded interactions: 796880 Sorted by model distance: nonbonded pdb=" NH1 ARG b 226 " pdb=" OD2 ASP g 32 " model vdw 2.059 2.520 nonbonded pdb=" O VAL D 122 " pdb=" ND2 ASNDC 322 " model vdw 2.123 2.520 nonbonded pdb=" OG1 THR c 55 " pdb=" OG SER f 26 " model vdw 2.133 2.440 nonbonded pdb=" O LEU G 260 " pdb=" NZ LYS M 245 " model vdw 2.142 2.520 nonbonded pdb=" O ILEDA 156 " pdb=" OG SERDA 266 " model vdw 2.154 2.440 ... (remaining 796875 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' } ncs_group { reference = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = (chain 'A' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'B' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'C' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'D' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'E' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'F' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'G' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'H' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'I' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'J' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'K' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'L' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'M' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'N' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'O' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'P' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'Q' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'R' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'S' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'T' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'U' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'V' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'W' and (resid 2 through 51 or resid 66 through 260)) selection = (chain 'X' and (resid 2 through 51 or resid 66 through 260)) } ncs_group { reference = chain 'DA' selection = chain 'DB' selection = chain 'DC' selection = chain 'DD' selection = chain 'DE' selection = chain 'DF' selection = chain 'DG' selection = chain 'DH' selection = chain 'DI' selection = chain 'DJ' selection = chain 'DK' } ncs_group { reference = (chain 'a' and resid 2 through 249) selection = chain 'b' selection = (chain 'c' and resid 2 through 249) selection = (chain 'd' and resid 2 through 249) selection = (chain 'e' and resid 2 through 249) } ncs_group { reference = (chain 'f' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'g' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'h' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'i' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'j' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'p' and (resid 2 through 53 or resid 59 through 132)) } ncs_group { reference = (chain 'k' and (resid 3 through 54 or resid 82 through 135)) selection = chain 'l' selection = chain 'm' selection = (chain 'n' and (resid 3 through 54 or resid 82 through 135)) selection = (chain 'o' and (resid 3 through 54 or resid 82 through 135)) } ncs_group { reference = (chain 'q' and resid 35 through 103) selection = (chain 'r' and resid 35 through 103) selection = (chain 's' and resid 35 through 103) selection = (chain 't' and resid 35 through 103) selection = (chain 'u' and resid 35 through 103) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.870 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: 0.090 Extract box with map and model: 32.680 Check model and map are aligned: 1.110 Set scattering table: 0.660 Process input model: 229.520 Find NCS groups from input model: 6.300 Set up NCS constraints: 0.890 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 284.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.003 0.059 102909 Z= 0.204 Angle : 0.480 14.690 139938 Z= 0.265 Chirality : 0.040 0.423 16520 Planarity : 0.003 0.041 18779 Dihedral : 10.349 89.858 37158 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.18 % 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: 0.97 (0.08), residues: 13465 helix: 3.57 (0.09), residues: 3498 sheet: -0.50 (0.09), residues: 3017 loop : -0.34 (0.08), residues: 6950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4065 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 3853 time to evaluate : 8.355 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 outliers start: 212 outliers final: 82 residues processed: 3972 average time/residue: 0.9077 time to fit residues: 6195.4351 Evaluate side-chains 2909 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 2827 time to evaluate : 8.364 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.7097 time to fit residues: 123.1993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 1135 optimal weight: 5.9990 chunk 1019 optimal weight: 9.9990 chunk 565 optimal weight: 0.3980 chunk 348 optimal weight: 6.9990 chunk 687 optimal weight: 0.0470 chunk 544 optimal weight: 4.9990 chunk 1054 optimal weight: 0.5980 chunk 407 optimal weight: 4.9990 chunk 641 optimal weight: 0.8980 chunk 784 optimal weight: 2.9990 chunk 1221 optimal weight: 4.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 125 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 88 GLN B 164 GLN C 32 ASN C 37 GLN C 59 GLN C 196 GLN D 88 GLN D 121 GLN F 67 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN G 121 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 121 GLN H 169 GLN I 83 GLN I 237 GLN J 121 GLN L 25 ASN L 162 GLN L 232 ASN M 137 GLN M 252 GLN N 37 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 ASN N 209 ASN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN O 51 GLN P 37 GLN P 85 ASN P 90 ASN P 121 GLN Q 32 ASN Q 51 GLN Q 252 GLN R 90 ASN R 121 GLN R 190 ASN R 259 GLN ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN T 135 GLN T 169 GLN T 209 ASN T 235 GLN U 252 GLN a 230 GLN b 116 GLN b 230 GLN d 25 ASN d 84 GLN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 246 GLN 5 324 ASN f 30 ASN g 113 GLN h 88 ASN j 17 GLN j 30 ASN j 113 GLN j 115 ASN l 17 ASN l 21 GLN l 92 GLN l 132 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 21 GLN ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN o 132 ASN p 30 ASN i 5 ASN i 22 ASN i 30 ASN i 115 ASN k 13 GLN k 32 ASN n 17 ASN n 21 GLN n 39 GLN n 135 GLN V 32 ASN V 169 GLN V 172 GLN X 67 GLN X 121 GLN ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 209 ASN q 83 GLN q 97 GLN r 55 GLN r 69 ASN ** r 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 90 ASN u 55 GLN DA 99 GLN ** DA 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 275 ASN ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 394 GLN ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 23 ASN DC 26 ASN DC 133 ASN DC 157 ASN ** DC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 392 GLN DD 23 ASN DD 68 ASN ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 97 ASN ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 280 ASN DE 352 ASN ** DF 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 68 ASN DF 338 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN DF 394 GLN DG 68 ASN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 314 GLN ** DH 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 314 GLN ** DH 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 394 GLN ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 89 ASN DJ 310 GLN DJ 314 GLN ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 401 ASN DK 319 ASN Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 102909 Z= 0.200 Angle : 0.547 9.906 139938 Z= 0.283 Chirality : 0.041 0.232 16520 Planarity : 0.003 0.042 18779 Dihedral : 3.472 21.114 14334 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 1.04 (0.07), residues: 13465 helix: 3.76 (0.08), residues: 3484 sheet: -0.47 (0.09), residues: 3063 loop : -0.36 (0.08), residues: 6918 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3305 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 2985 time to evaluate : 8.403 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 outliers start: 320 outliers final: 168 residues processed: 3155 average time/residue: 0.9655 time to fit residues: 5256.7830 Evaluate side-chains 2929 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 2761 time to evaluate : 8.457 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 0 residues processed: 168 average time/residue: 0.7832 time to fit residues: 260.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 678 optimal weight: 0.7980 chunk 379 optimal weight: 3.9990 chunk 1016 optimal weight: 3.9990 chunk 831 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 chunk 1223 optimal weight: 0.8980 chunk 1321 optimal weight: 40.0000 chunk 1089 optimal weight: 30.0000 chunk 1213 optimal weight: 0.7980 chunk 417 optimal weight: 7.9990 chunk 981 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 85 ASN A 121 GLN E 16 GLN E 121 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN H 121 GLN I 83 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN L 162 GLN M 121 GLN M 252 GLN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 ASN N 259 GLN O 83 GLN O 145 ASN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN Q 47 GLN Q 252 GLN S 137 GLN T 135 GLN T 235 GLN a 18 GLN a 240 ASN ** a 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 GLN ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 230 GLN g 113 GLN ** h 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 17 GLN j 113 GLN j 115 ASN l 21 GLN l 132 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN i 115 ASN k 32 ASN n 21 GLN n 39 GLN V 90 ASN X 81 HIS X 121 GLN ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 90 ASN s 87 GLN t 90 ASN ** v 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 329 GLN ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN DA 394 GLN DB 68 ASN ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 268 GLN ** DC 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 97 ASN ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 338 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN DF 394 GLN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DH 23 ASN ** DH 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 99 GLN DH 130 GLN ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 280 ASN DH 322 ASN ** DH 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 5 GLN ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 157 ASN DI 338 GLN DI 374 ASN DJ 89 ASN DJ 99 GLN DJ 401 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 102909 Z= 0.162 Angle : 0.515 10.629 139938 Z= 0.265 Chirality : 0.040 0.246 16520 Planarity : 0.003 0.048 18779 Dihedral : 3.449 21.313 14334 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 1.05 (0.07), residues: 13465 helix: 3.75 (0.08), residues: 3486 sheet: -0.45 (0.09), residues: 3064 loop : -0.35 (0.08), residues: 6915 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3163 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 2903 time to evaluate : 8.402 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 outliers start: 260 outliers final: 125 residues processed: 3039 average time/residue: 0.9158 time to fit residues: 4779.4202 Evaluate side-chains 2837 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 2712 time to evaluate : 8.296 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 0 residues processed: 125 average time/residue: 0.7284 time to fit residues: 185.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 1208 optimal weight: 4.9990 chunk 919 optimal weight: 30.0000 chunk 635 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 583 optimal weight: 3.9990 chunk 821 optimal weight: 1.9990 chunk 1227 optimal weight: 4.9990 chunk 1300 optimal weight: 9.9990 chunk 641 optimal weight: 2.9990 chunk 1163 optimal weight: 7.9990 chunk 350 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 196 GLN A 252 GLN B 51 GLN B 67 GLN B 104 GLN C 59 GLN C 162 GLN C 174 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN F 137 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN G 121 GLN H 121 GLN I 252 GLN J 37 GLN J 67 GLN K 47 GLN K 121 GLN L 162 GLN L 169 GLN M 85 ASN M 235 GLN M 252 GLN ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 GLN N 259 GLN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN Q 252 GLN R 243 ASN S 47 GLN T 259 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 240 ASN c 116 GLN d 25 ASN ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 ASN ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN j 113 GLN j 115 ASN l 17 ASN l 21 GLN l 92 GLN l 132 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 21 GLN ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN i 115 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN X 47 GLN q 97 GLN r 55 GLN r 90 ASN t 90 ASN u 55 GLN v 90 ASN DB 22 ASN DB 26 ASN DB 68 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 319 ASN DB 352 ASN DB 394 GLN DC 274 ASN DC 319 ASN DC 385 ASN DC 392 GLN ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 97 ASN ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 338 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 394 GLN DG 5 GLN DG 68 ASN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 280 ASN DG 282 ASN ** DG 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 379 GLN DG 383 GLN DG 397 ASN DG 401 ASN ** DH 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 374 ASN DJ 23 ASN DJ 89 ASN DJ 308 GLN DK 26 ASN DK 213 HIS Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 102909 Z= 0.409 Angle : 0.629 10.842 139938 Z= 0.328 Chirality : 0.044 0.229 16520 Planarity : 0.004 0.052 18779 Dihedral : 4.063 25.626 14334 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.00 % Favored : 94.99 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.65 (0.07), residues: 13465 helix: 3.22 (0.08), residues: 3491 sheet: -0.68 (0.09), residues: 3137 loop : -0.48 (0.08), residues: 6837 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3178 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 2759 time to evaluate : 8.399 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 outliers start: 419 outliers final: 251 residues processed: 2986 average time/residue: 0.9113 time to fit residues: 4672.5444 Evaluate side-chains 2871 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 2620 time to evaluate : 8.526 Switching outliers to nearest non-outliers outliers start: 251 outliers final: 0 residues processed: 251 average time/residue: 0.7170 time to fit residues: 352.9904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 1082 optimal weight: 7.9990 chunk 738 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 968 optimal weight: 0.8980 chunk 536 optimal weight: 0.9980 chunk 1109 optimal weight: 1.9990 chunk 898 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 663 optimal weight: 5.9990 chunk 1166 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 196 GLN B 51 GLN B 104 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 196 GLN E 51 GLN E 121 GLN E 252 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 174 ASN H 121 GLN I 252 GLN K 121 GLN K 209 ASN L 25 ASN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 259 GLN N 100 GLN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 259 GLN P 174 ASN P 196 GLN R 90 ASN R 137 GLN R 243 ASN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 GLN T 104 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN j 17 GLN j 115 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 21 GLN ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN i 115 ASN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN V 16 GLN V 28 ASN V 47 GLN W 135 GLN X 252 GLN q 97 GLN r 90 ASN t 83 GLN t 90 ASN ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 374 ASN DA 381 ASN DA 394 GLN DB 129 GLN DB 394 GLN ** DC 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 387 GLN DC 392 GLN DE 79 GLN ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 99 GLN ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN DF 394 GLN DG 112 GLN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 338 GLN DH 197 ASN ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN DH 314 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 268 GLN DJ 319 ASN ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 102909 Z= 0.220 Angle : 0.555 10.415 139938 Z= 0.286 Chirality : 0.041 0.209 16520 Planarity : 0.003 0.048 18779 Dihedral : 3.814 23.798 14334 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.84 % Favored : 96.15 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.82 (0.07), residues: 13465 helix: 3.49 (0.08), residues: 3490 sheet: -0.57 (0.09), residues: 2981 loop : -0.47 (0.08), residues: 6994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2951 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 2761 time to evaluate : 8.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 107 residues processed: 2863 average time/residue: 0.8943 time to fit residues: 4382.2517 Evaluate side-chains 2738 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 2631 time to evaluate : 8.197 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.7115 time to fit residues: 155.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 437 optimal weight: 2.9990 chunk 1170 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 763 optimal weight: 0.0970 chunk 320 optimal weight: 7.9990 chunk 1301 optimal weight: 0.5980 chunk 1080 optimal weight: 10.0000 chunk 602 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 430 optimal weight: 10.0000 chunk 683 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 255 GLN C 259 GLN D 209 ASN E 51 GLN E 121 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN H 121 GLN H 196 GLN I 237 GLN K 88 GLN K 90 ASN K 121 GLN L 162 GLN M 90 ASN M 252 GLN M 259 GLN N 235 GLN N 259 GLN O 259 GLN P 121 GLN P 174 ASN R 90 ASN T 104 GLN T 235 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 ASN g 113 GLN ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 113 GLN j 115 ASN l 17 ASN l 21 GLN l 132 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 21 GLN ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN k 13 GLN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN q 49 GLN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 55 GLN r 90 ASN ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN DA 394 GLN DB 112 GLN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 394 GLN DC 322 ASN DC 387 GLN ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN DF 394 GLN DG 68 ASN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 379 GLN ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.075 102909 Z= 0.162 Angle : 0.537 10.777 139938 Z= 0.275 Chirality : 0.041 0.184 16520 Planarity : 0.003 0.049 18779 Dihedral : 3.614 22.579 14334 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.93 (0.07), residues: 13465 helix: 3.65 (0.08), residues: 3493 sheet: -0.56 (0.09), residues: 3089 loop : -0.41 (0.08), residues: 6883 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2947 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 2775 time to evaluate : 8.173 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 outliers start: 172 outliers final: 86 residues processed: 2846 average time/residue: 0.9345 time to fit residues: 4567.8494 Evaluate side-chains 2740 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 2654 time to evaluate : 8.158 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.7307 time to fit residues: 129.1193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 1254 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 741 optimal weight: 4.9990 chunk 950 optimal weight: 7.9990 chunk 736 optimal weight: 2.9990 chunk 1095 optimal weight: 5.9990 chunk 726 optimal weight: 0.8980 chunk 1296 optimal weight: 7.9990 chunk 811 optimal weight: 3.9990 chunk 790 optimal weight: 1.9990 chunk 598 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN D 196 GLN ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN I 67 GLN K 121 GLN L 25 ASN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 259 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN a 240 ASN c 116 GLN d 106 GLN ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN ** j 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 113 GLN j 115 ASN ** l 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 21 GLN ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN i 17 GLN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN W 37 GLN X 28 ASN X 252 GLN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 55 GLN r 90 ASN t 49 GLN t 90 ASN u 55 GLN ** u 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 319 ASN ** DC 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DD 11 ASN DD 68 ASN ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 268 GLN DF 155 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 194 HIS ** DG 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 401 ASN ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 102909 Z= 0.387 Angle : 0.614 11.236 139938 Z= 0.317 Chirality : 0.043 0.242 16520 Planarity : 0.004 0.055 18779 Dihedral : 3.909 20.813 14334 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.75 % Favored : 95.24 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.72 (0.07), residues: 13465 helix: 3.35 (0.08), residues: 3492 sheet: -0.56 (0.09), residues: 3204 loop : -0.52 (0.08), residues: 6769 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2845 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 2654 time to evaluate : 7.342 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 outliers start: 191 outliers final: 123 residues processed: 2743 average time/residue: 0.8737 time to fit residues: 4089.4247 Evaluate side-chains 2720 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 2597 time to evaluate : 7.413 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 0 residues processed: 123 average time/residue: 0.6624 time to fit residues: 165.2012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 802 optimal weight: 0.8980 chunk 517 optimal weight: 3.9990 chunk 774 optimal weight: 0.9980 chunk 390 optimal weight: 0.8980 chunk 254 optimal weight: 0.4980 chunk 251 optimal weight: 1.9990 chunk 824 optimal weight: 3.9990 chunk 883 optimal weight: 1.9990 chunk 640 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 1018 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 259 GLN E 121 GLN E 137 GLN E 252 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 GLN I 252 GLN K 88 GLN K 121 GLN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 137 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 235 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN ** h 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 ASN l 21 GLN l 23 GLN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN i 104 ASN k 13 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 55 GLN r 90 ASN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN DB 26 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 295 ASN DD 68 ASN ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 206 ASN DF 268 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN DG 68 ASN ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 213 HIS ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 129 GLN ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 365 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 102909 Z= 0.179 Angle : 0.566 13.083 139938 Z= 0.288 Chirality : 0.041 0.231 16520 Planarity : 0.003 0.056 18779 Dihedral : 3.685 22.230 14334 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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 (0.07), residues: 13465 helix: 3.58 (0.08), residues: 3496 sheet: -0.66 (0.09), residues: 3115 loop : -0.40 (0.08), residues: 6854 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2846 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 2758 time to evaluate : 7.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 50 residues processed: 2791 average time/residue: 0.8663 time to fit residues: 4141.9581 Evaluate side-chains 2707 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 2657 time to evaluate : 8.492 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.6768 time to fit residues: 73.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 1179 optimal weight: 20.0000 chunk 1241 optimal weight: 4.9990 chunk 1133 optimal weight: 20.0000 chunk 1208 optimal weight: 5.9990 chunk 727 optimal weight: 1.9990 chunk 526 optimal weight: 1.9990 chunk 948 optimal weight: 0.9980 chunk 370 optimal weight: 5.9990 chunk 1091 optimal weight: 5.9990 chunk 1142 optimal weight: 0.9980 chunk 1203 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 196 GLN A 225 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 209 ASN E 121 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 121 GLN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 259 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 ASN l 21 GLN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN ** n 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 55 GLN r 83 GLN r 90 ASN u 55 GLN ** u 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 319 ASN ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 397 ASN DJ 401 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 102909 Z= 0.317 Angle : 0.614 13.213 139938 Z= 0.315 Chirality : 0.042 0.241 16520 Planarity : 0.004 0.055 18779 Dihedral : 3.874 20.809 14334 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.72 (0.07), residues: 13465 helix: 3.36 (0.08), residues: 3496 sheet: -0.59 (0.09), residues: 3264 loop : -0.51 (0.08), residues: 6705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2772 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 2682 time to evaluate : 7.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 57 residues processed: 2716 average time/residue: 0.8446 time to fit residues: 3926.9362 Evaluate side-chains 2670 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 2613 time to evaluate : 7.276 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.6254 time to fit residues: 78.2211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 793 optimal weight: 0.9990 chunk 1277 optimal weight: 0.0040 chunk 779 optimal weight: 0.5980 chunk 606 optimal weight: 2.9990 chunk 888 optimal weight: 3.9990 chunk 1339 optimal weight: 20.0000 chunk 1233 optimal weight: 1.9990 chunk 1067 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 824 optimal weight: 0.8980 chunk 654 optimal weight: 5.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 209 ASN E 137 GLN F 51 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN H 121 GLN K 100 GLN K 121 GLN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN M 90 ASN M 100 GLN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 GLN O 259 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 137 GLN R 259 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 235 GLN T 259 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN ** i 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 ASN ** n 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 135 GLN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN s 49 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 83 GLN ** DA 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN ** DB 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN ** DG 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 397 ASN ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 102909 Z= 0.191 Angle : 0.588 13.043 139938 Z= 0.299 Chirality : 0.041 0.251 16520 Planarity : 0.003 0.053 18779 Dihedral : 3.711 22.214 14334 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % 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: 0.86 (0.07), residues: 13465 helix: 3.54 (0.08), residues: 3495 sheet: -0.48 (0.09), residues: 3178 loop : -0.48 (0.08), residues: 6792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26930 Ramachandran restraints generated. 13465 Oldfield, 0 Emsley, 13465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2802 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 2749 time to evaluate : 7.457 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 outliers start: 53 outliers final: 34 residues processed: 2768 average time/residue: 0.8482 time to fit residues: 4017.8740 Evaluate side-chains 2689 residues out of total 11022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 2655 time to evaluate : 7.291 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6814 time to fit residues: 53.6446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1345 random chunks: chunk 847 optimal weight: 0.8980 chunk 1136 optimal weight: 0.9980 chunk 326 optimal weight: 8.9990 chunk 983 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 296 optimal weight: 0.4980 chunk 1068 optimal weight: 2.9990 chunk 447 optimal weight: 0.3980 chunk 1097 optimal weight: 8.9990 chunk 135 optimal weight: 0.0980 chunk 196 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 209 ASN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 121 GLN L 162 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 235 GLN M 252 GLN N 235 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 GLN O 259 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 259 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 259 GLN ** a 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 ASN ** e 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 GLN ** i 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 ASN W 145 ASN X 67 GLN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN r 55 GLN ** s 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 55 GLN ** u 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 GLN ** DA 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN DB 26 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 319 ASN DD 68 ASN ** DD 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 89 ASN ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 381 ASN ** DG 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 268 GLN ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 112 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104420 restraints weight = 171683.893| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.69 r_work: 0.3197 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 102909 Z= 0.172 Angle : 0.588 13.065 139938 Z= 0.297 Chirality : 0.041 0.256 16520 Planarity : 0.003 0.059 18779 Dihedral : 3.598 22.969 14334 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.07), residues: 13465 helix: 3.57 (0.08), residues: 3490 sheet: -0.57 (0.09), residues: 3057 loop : -0.41 (0.08), residues: 6918 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55317.91 seconds wall clock time: 949 minutes 31.78 seconds (56971.78 seconds total)