Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 22:05:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e80_31006/10_2023/7e80_31006.pdb" } resolution = 3.67 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= -0.001 sd= 0.092 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 456 5.16 5 C 71253 2.51 5 N 19749 2.21 5 O 23010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 58": "OE1" <-> "OE2" 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: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 114468 Number of models: 1 Model: "" Number of chains: 77 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} Chain: "CE" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2002 Classifications: {'peptide': 260} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 242} Chain: "CA" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "CB" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "CC" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "CD" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "w" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1636 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "x" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1636 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "y" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1636 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "z" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1636 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "CF" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1636 Classifications: {'peptide': 211} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 194} Time building chain proxies: 43.85, per 1000 atoms: 0.38 Number of scatterers: 114468 At special positions: 0 Unit cell: (190.822, 192.129, 433.924, 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 456 16.00 O 23010 8.00 N 19749 7.00 C 71253 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: 33.21 Conformation dependent library (CDL) restraints added in 12.3 seconds 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28052 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 380 sheets defined 33.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 removed outlier: 3.652A pdb=" N ASN A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.501A pdb=" N GLY A 183 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 259 removed outlier: 3.630A pdb=" N GLU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.189A 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: 3.634A pdb=" N VAL B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 28 removed outlier: 3.634A 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: 3.649A pdb=" N ASN D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 184 removed outlier: 3.542A pdb=" N LEU D 184 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 259 removed outlier: 3.646A 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: 3.754A pdb=" N LEU E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.667A 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: 3.772A 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: 3.581A 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: 4.397A 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: 3.837A pdb=" N GLY J 199 " --> pdb=" O GLN J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 258 removed outlier: 4.379A pdb=" N VAL J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 28 removed outlier: 3.770A 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: 3.728A pdb=" N GLU L 229 " --> pdb=" O ASN L 225 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 230 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.884A 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: 4.014A 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: 3.770A 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: 3.694A 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: 3.719A 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: 4.449A pdb=" N VAL P 231 " --> pdb=" O ALA P 227 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.534A pdb=" N GLY Q 183 " --> pdb=" O ASN Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 260 removed outlier: 4.183A pdb=" N VAL Q 231 " --> pdb=" O ALA Q 227 " (cutoff:3.500A) removed outlier: 3.574A 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: 3.570A 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: 3.879A 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: 3.644A 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: 3.694A 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: 3.561A 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: 3.687A pdb=" N ALA a 8 " --> pdb=" O ALA a 4 " (cutoff:3.500A) removed outlier: 3.669A 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: 4.346A 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: 3.896A 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: 3.684A 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: 4.607A 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: 4.152A 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: 3.716A 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: 3.993A 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: 5.104A 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: 3.613A 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: 4.023A pdb=" N THR W 10 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.820A 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: 3.631A pdb=" N VALDB 373 " --> pdb=" O SERDB 369 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.589A 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: 3.702A pdb=" N ILEDD 389 " --> pdb=" O ASNDD 385 " (cutoff:3.500A) removed outlier: 4.112A 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: 3.605A 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: 3.701A 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: 3.567A 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: 3.505A 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: 3.690A pdb=" N THRDH 398 " --> pdb=" O GLNDH 394 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.619A pdb=" N LEUDK 10 " --> pdb=" O ALADK 6 " (cutoff:3.500A) Processing helix chain 'DK' and resid 174 through 178 removed outlier: 3.966A pdb=" N SERDK 177 " --> pdb=" O ASPDK 174 " (cutoff:3.500A) removed outlier: 4.184A 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: 3.729A 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 helix chain 'CE' and resid 8 through 17 removed outlier: 3.817A pdb=" N HISCE 14 " --> pdb=" O LEUCE 10 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEUCE 15 " --> pdb=" O TYRCE 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHECE 17 " --> pdb=" O LEUCE 13 " (cutoff:3.500A) Processing helix chain 'CE' and resid 17 through 30 removed outlier: 4.271A pdb=" N LEUCE 21 " --> pdb=" O PHECE 17 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARGCE 22 " --> pdb=" O TRPCE 18 " (cutoff:3.500A) Processing helix chain 'CE' and resid 39 through 55 removed outlier: 4.099A pdb=" N GLYCE 47 " --> pdb=" O LYSCE 43 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILECE 48 " --> pdb=" O LEUCE 44 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILECE 50 " --> pdb=" O LEUCE 46 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEUCE 52 " --> pdb=" O ILECE 48 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VALCE 53 " --> pdb=" O METCE 49 " (cutoff:3.500A) Processing helix chain 'CE' and resid 67 through 105 removed outlier: 3.562A pdb=" N TRPCE 72 " --> pdb=" O ILECE 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEUCE 79 " --> pdb=" O METCE 75 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILECE 80 " --> pdb=" O GLNCE 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLYCE 81 " --> pdb=" O GLNCE 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N METCE 88 " --> pdb=" O LEUCE 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLNCE 89 " --> pdb=" O GLYCE 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHECE 90 " --> pdb=" O PHECE 86 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALACE 91 " --> pdb=" O THRCE 87 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHECE 92 " --> pdb=" O METCE 88 " (cutoff:3.500A) Processing helix chain 'CE' and resid 109 through 113 removed outlier: 3.934A pdb=" N PHECE 113 " --> pdb=" O PHECE 110 " (cutoff:3.500A) Processing helix chain 'CE' and resid 121 through 126 removed outlier: 4.499A pdb=" N LEUCE 125 " --> pdb=" O ASNCE 121 " (cutoff:3.500A) Processing helix chain 'CE' and resid 126 through 131 Processing helix chain 'CE' and resid 131 through 141 removed outlier: 3.893A pdb=" N LEUCE 135 " --> pdb=" O METCE 131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUCE 136 " --> pdb=" O LEUCE 132 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHECE 140 " --> pdb=" O LEUCE 136 " (cutoff:3.500A) Processing helix chain 'CE' and resid 143 through 157 Processing helix chain 'CE' and resid 168 through 174 Processing helix chain 'CE' and resid 177 through 187 removed outlier: 3.548A pdb=" N GLYCE 183 " --> pdb=" O ILECE 179 " (cutoff:3.500A) Processing helix chain 'CE' and resid 187 through 203 Processing helix chain 'CE' and resid 204 through 206 No H-bonds generated for 'chain 'CE' and resid 204 through 206' Processing helix chain 'CE' and resid 216 through 232 removed outlier: 3.640A pdb=" N THRCE 223 " --> pdb=" O PROCE 219 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VALCE 224 " --> pdb=" O LEUCE 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALACE 230 " --> pdb=" O ILECE 226 " (cutoff:3.500A) Processing helix chain 'CE' and resid 232 through 262 removed outlier: 3.599A pdb=" N ILECE 236 " --> pdb=" O LEUCE 232 " (cutoff:3.500A) Proline residue: CE 238 - end of helix removed outlier: 4.276A pdb=" N GLUCE 241 " --> pdb=" O ALACE 237 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUCE 243 " --> pdb=" O PHECE 239 " (cutoff:3.500A) Proline residue: CE 259 - end of helix removed outlier: 3.677A pdb=" N ASNCE 262 " --> pdb=" O METCE 258 " (cutoff:3.500A) Processing helix chain 'CA' and resid 2 through 39 removed outlier: 3.504A pdb=" N VALCA 6 " --> pdb=" O THRCA 2 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N METCA 9 " --> pdb=" O SERCA 5 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLYCA 10 " --> pdb=" O VALCA 6 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLUCA 12 " --> pdb=" O METCA 8 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALACA 13 " --> pdb=" O METCA 9 " (cutoff:3.500A) Proline residue: CA 23 - end of helix Processing helix chain 'CA' and resid 50 through 66 removed outlier: 3.755A pdb=" N ILECA 63 " --> pdb=" O PHECA 59 " (cutoff:3.500A) Processing helix chain 'CA' and resid 66 through 83 removed outlier: 4.001A pdb=" N LEUCA 73 " --> pdb=" O METCA 69 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEUCA 74 " --> pdb=" O LEUCA 70 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASPCA 75 " --> pdb=" O ASNCA 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYRCA 76 " --> pdb=" O LEUCA 72 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGCA 78 " --> pdb=" O LEUCA 74 " (cutoff:3.500A) Processing helix chain 'CA' and resid 83 through 88 removed outlier: 4.179A pdb=" N ILECA 88 " --> pdb=" O LEUCA 84 " (cutoff:3.500A) Processing helix chain 'CB' and resid 2 through 39 removed outlier: 3.904A pdb=" N VALCB 6 " --> pdb=" O THRCB 2 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALACB 17 " --> pdb=" O ALACB 13 " (cutoff:3.500A) Proline residue: CB 23 - end of helix Processing helix chain 'CB' and resid 50 through 66 removed outlier: 3.606A pdb=" N LYSCB 54 " --> pdb=" O SERCB 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALCB 56 " --> pdb=" O ILECB 52 " (cutoff:3.500A) Processing helix chain 'CB' and resid 66 through 83 removed outlier: 3.751A pdb=" N LEUCB 70 " --> pdb=" O GLYCB 66 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEUCB 73 " --> pdb=" O METCB 69 " (cutoff:3.500A) Processing helix chain 'CB' and resid 83 through 88 removed outlier: 3.672A pdb=" N ILECB 88 " --> pdb=" O LEUCB 84 " (cutoff:3.500A) Processing helix chain 'CC' and resid 2 through 39 removed outlier: 3.713A pdb=" N VALCC 6 " --> pdb=" O THRCC 2 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N METCC 7 " --> pdb=" O PROCC 3 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALACC 17 " --> pdb=" O ALACC 13 " (cutoff:3.500A) Proline residue: CC 23 - end of helix removed outlier: 3.968A pdb=" N VALCC 27 " --> pdb=" O PROCC 23 " (cutoff:3.500A) Processing helix chain 'CC' and resid 50 through 66 removed outlier: 3.638A pdb=" N LYSCC 54 " --> pdb=" O SERCC 50 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VALCC 56 " --> pdb=" O ILECC 52 " (cutoff:3.500A) Processing helix chain 'CC' and resid 66 through 88 removed outlier: 3.578A pdb=" N LEUCC 72 " --> pdb=" O TRPCC 68 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEUCC 73 " --> pdb=" O METCC 69 " (cutoff:3.500A) Proline residue: CC 85 - end of helix removed outlier: 3.858A pdb=" N ILECC 88 " --> pdb=" O LEUCC 84 " (cutoff:3.500A) Processing helix chain 'CD' and resid 2 through 39 Proline residue: CD 23 - end of helix Processing helix chain 'CD' and resid 50 through 83 Proline residue: CD 67 - end of helix removed outlier: 4.280A pdb=" N LEUCD 73 " --> pdb=" O METCD 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUCD 74 " --> pdb=" O LEUCD 70 " (cutoff:3.500A) Processing helix chain 'CD' and resid 83 through 88 removed outlier: 3.906A pdb=" N ILECD 88 " --> pdb=" O LEUCD 84 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 61 removed outlier: 3.679A pdb=" N LEU w 45 " --> pdb=" O SER w 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR w 52 " --> pdb=" O ILE w 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE w 53 " --> pdb=" O THR w 49 " (cutoff:3.500A) Proline residue: w 55 - end of helix removed outlier: 3.505A pdb=" N LEU w 58 " --> pdb=" O LEU w 54 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU w 59 " --> pdb=" O PRO w 55 " (cutoff:3.500A) Processing helix chain 'w' and resid 64 through 78 Processing helix chain 'w' and resid 85 through 118 Proline residue: w 103 - end of helix Proline residue: w 115 - end of helix Processing helix chain 'w' and resid 122 through 142 removed outlier: 3.764A pdb=" N ASP w 128 " --> pdb=" O GLN w 124 " (cutoff:3.500A) Proline residue: w 133 - end of helix removed outlier: 3.678A pdb=" N GLN w 141 " --> pdb=" O PHE w 137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR w 142 " --> pdb=" O MET w 138 " (cutoff:3.500A) Processing helix chain 'w' and resid 144 through 155 Processing helix chain 'w' and resid 166 through 208 removed outlier: 3.822A pdb=" N LEU w 171 " --> pdb=" O MET w 167 " (cutoff:3.500A) Proline residue: w 172 - end of helix removed outlier: 3.844A pdb=" N PHE w 183 " --> pdb=" O LEU w 179 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN w 184 " --> pdb=" O LYS w 180 " (cutoff:3.500A) Proline residue: w 192 - end of helix Processing helix chain 'w' and resid 213 through 229 removed outlier: 3.598A pdb=" N ILE w 217 " --> pdb=" O PRO w 213 " (cutoff:3.500A) Proline residue: w 220 - end of helix Processing helix chain 'w' and resid 230 through 245 Processing helix chain 'x' and resid 39 through 60 Proline residue: x 55 - end of helix Processing helix chain 'x' and resid 64 through 78 removed outlier: 3.724A pdb=" N ILE x 68 " --> pdb=" O PHE x 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 118 Proline residue: x 103 - end of helix Proline residue: x 115 - end of helix removed outlier: 4.145A pdb=" N GLU x 118 " --> pdb=" O GLN x 114 " (cutoff:3.500A) Processing helix chain 'x' and resid 122 through 142 removed outlier: 4.725A pdb=" N ASP x 128 " --> pdb=" O GLN x 124 " (cutoff:3.500A) Proline residue: x 133 - end of helix removed outlier: 3.824A pdb=" N ARG x 140 " --> pdb=" O ALA x 136 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN x 141 " --> pdb=" O PHE x 137 " (cutoff:3.500A) Processing helix chain 'x' and resid 143 through 154 Processing helix chain 'x' and resid 166 through 207 removed outlier: 3.501A pdb=" N LEU x 171 " --> pdb=" O MET x 167 " (cutoff:3.500A) Proline residue: x 172 - end of helix Proline residue: x 192 - end of helix removed outlier: 3.580A pdb=" N LEU x 207 " --> pdb=" O VAL x 203 " (cutoff:3.500A) Processing helix chain 'x' and resid 214 through 229 Proline residue: x 220 - end of helix Processing helix chain 'x' and resid 230 through 245 removed outlier: 3.601A pdb=" N LEU x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 3.655A pdb=" N THR y 52 " --> pdb=" O ILE y 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE y 53 " --> pdb=" O THR y 49 " (cutoff:3.500A) Proline residue: y 55 - end of helix removed outlier: 3.867A pdb=" N LEU y 59 " --> pdb=" O PRO y 55 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 78 Processing helix chain 'y' and resid 85 through 101 Processing helix chain 'y' and resid 101 through 118 removed outlier: 4.956A pdb=" N GLN y 114 " --> pdb=" O VAL y 110 " (cutoff:3.500A) Proline residue: y 115 - end of helix removed outlier: 3.630A pdb=" N GLU y 118 " --> pdb=" O GLN y 114 " (cutoff:3.500A) Processing helix chain 'y' and resid 122 through 141 removed outlier: 4.210A pdb=" N ASP y 128 " --> pdb=" O GLN y 124 " (cutoff:3.500A) Proline residue: y 133 - end of helix Processing helix chain 'y' and resid 143 through 155 Processing helix chain 'y' and resid 161 through 165 removed outlier: 3.626A pdb=" N VAL y 165 " --> pdb=" O PRO y 162 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 206 Proline residue: y 172 - end of helix removed outlier: 3.785A pdb=" N THR y 188 " --> pdb=" O GLN y 184 " (cutoff:3.500A) Proline residue: y 192 - end of helix Processing helix chain 'y' and resid 214 through 230 Proline residue: y 220 - end of helix Processing helix chain 'y' and resid 230 through 244 Processing helix chain 'z' and resid 39 through 58 removed outlier: 3.754A pdb=" N LEU z 51 " --> pdb=" O PHE z 47 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR z 52 " --> pdb=" O ILE z 48 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE z 53 " --> pdb=" O THR z 49 " (cutoff:3.500A) Proline residue: z 55 - end of helix Processing helix chain 'z' and resid 64 through 78 Processing helix chain 'z' and resid 85 through 101 Processing helix chain 'z' and resid 101 through 118 Proline residue: z 115 - end of helix removed outlier: 4.432A pdb=" N GLU z 118 " --> pdb=" O GLN z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 122 through 142 removed outlier: 4.069A pdb=" N ASP z 128 " --> pdb=" O GLN z 124 " (cutoff:3.500A) Proline residue: z 133 - end of helix removed outlier: 3.588A pdb=" N ARG z 140 " --> pdb=" O ALA z 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN z 141 " --> pdb=" O PHE z 137 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 155 removed outlier: 3.724A pdb=" N LEU z 147 " --> pdb=" O ARG z 143 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA z 148 " --> pdb=" O GLU z 144 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU z 149 " --> pdb=" O ALA z 145 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 208 removed outlier: 3.701A pdb=" N LEU z 171 " --> pdb=" O MET z 167 " (cutoff:3.500A) Proline residue: z 172 - end of helix Proline residue: z 192 - end of helix removed outlier: 4.006A pdb=" N GLY z 208 " --> pdb=" O LEU z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 213 through 230 removed outlier: 3.655A pdb=" N ILE z 217 " --> pdb=" O PRO z 213 " (cutoff:3.500A) Proline residue: z 220 - end of helix Processing helix chain 'z' and resid 230 through 245 removed outlier: 3.690A pdb=" N LEU z 234 " --> pdb=" O ASP z 230 " (cutoff:3.500A) Processing helix chain 'CF' and resid 39 through 53 removed outlier: 3.626A pdb=" N PHECF 53 " --> pdb=" O THRCF 49 " (cutoff:3.500A) Processing helix chain 'CF' and resid 53 through 58 removed outlier: 3.683A pdb=" N LEUCF 58 " --> pdb=" O LEUCF 54 " (cutoff:3.500A) Processing helix chain 'CF' and resid 64 through 79 removed outlier: 3.825A pdb=" N ILECF 69 " --> pdb=" O THRCF 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLYCF 79 " --> pdb=" O ARGCF 75 " (cutoff:3.500A) Processing helix chain 'CF' and resid 85 through 101 removed outlier: 3.530A pdb=" N GLYCF 91 " --> pdb=" O GLNCF 87 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHECF 95 " --> pdb=" O GLYCF 91 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) Processing helix chain 'CF' and resid 101 through 112 Processing helix chain 'CF' and resid 112 through 119 Processing helix chain 'CF' and resid 122 through 141 removed outlier: 3.605A pdb=" N LEUCF 127 " --> pdb=" O METCF 123 " (cutoff:3.500A) Proline residue: CF 133 - end of helix Processing helix chain 'CF' and resid 146 through 154 removed outlier: 3.905A pdb=" N PHECF 150 " --> pdb=" O ASPCF 146 " (cutoff:3.500A) Processing helix chain 'CF' and resid 166 through 207 removed outlier: 3.544A pdb=" N LEUCF 170 " --> pdb=" O PROCF 166 " (cutoff:3.500A) Proline residue: CF 172 - end of helix removed outlier: 3.706A pdb=" N THRCF 188 " --> pdb=" O GLNCF 184 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILECF 189 " --> pdb=" O ILECF 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILECF 191 " --> pdb=" O PHECF 187 " (cutoff:3.500A) Proline residue: CF 192 - end of helix removed outlier: 3.839A pdb=" N LEUCF 204 " --> pdb=" O ILECF 200 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N METCF 205 " --> pdb=" O ALACF 201 " (cutoff:3.500A) Processing helix chain 'CF' and resid 213 through 229 removed outlier: 4.302A pdb=" N ILECF 217 " --> pdb=" O PROCF 213 " (cutoff:3.500A) Proline residue: CF 220 - end of helix Processing helix chain 'CF' and resid 230 through 245 removed outlier: 3.845A pdb=" N LEUCF 234 " --> pdb=" O ASPCF 230 " (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: 3.550A pdb=" N VAL A 136 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.054A 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: 3.550A 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: 3.973A 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: 4.497A pdb=" N THR B 77 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.234A 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: 7.018A 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: 3.988A pdb=" N GLU B 185 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 193 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.774A 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: 6.371A 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: 3.604A 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: 3.796A 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: 5.521A 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: 3.694A pdb=" N SER D 148 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 7.007A 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: 6.285A 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: 4.330A 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: 3.572A 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: 3.583A 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: 4.101A 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: 6.415A 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: 6.339A 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: 7.218A 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: 4.194A 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: 3.884A 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: 4.331A 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: 6.621A pdb=" N ARG L 38 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 4.723A 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: 6.397A 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: 6.135A pdb=" N ARG M 38 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR M 77 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 7.034A 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: 4.078A 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: 3.613A 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: 4.829A 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: 7.397A 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: 3.697A 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: 6.564A 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: 7.079A 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: 4.563A 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: 5.547A 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: 3.973A 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: 3.863A 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: 4.098A 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: 6.772A pdb=" N VAL S 159 " --> pdb=" O GLN S 169 " (cutoff:3.500A) removed outlier: 5.624A 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: 4.231A 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: 6.316A 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: 6.920A 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: 6.921A 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: 3.626A 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: 6.654A 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: 6.482A 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: 3.560A 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: 6.689A 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 '7' and resid 316 through 317 Processing sheet with id=AY6, first strand: chain '9' and resid 316 through 317 Processing sheet with id=AY7, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.256A pdb=" N GLN f 46 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 4.758A 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=AY8, first strand: chain 'f' and resid 75 through 78 Processing sheet with id=AY9, 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=AZ1, first strand: chain 'g' and resid 75 through 78 Processing sheet with id=AZ2, 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=AZ3, first strand: chain 'h' and resid 77 through 78 Processing sheet with id=AZ4, 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: 5.450A pdb=" N VAL j 64 " --> pdb=" O GLN j 50 " (cutoff:3.500A) Processing sheet with id=AZ5, first strand: chain 'j' and resid 76 through 78 Processing sheet with id=AZ6, first strand: chain 'l' and resid 41 through 42 Processing sheet with id=AZ7, 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: 4.617A 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=AZ8, first strand: chain 'p' and resid 75 through 78 Processing sheet with id=AZ9, 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: 6.752A pdb=" N VAL i 48 " --> pdb=" O ALA i 65 " (cutoff:3.500A) Processing sheet with id=BA1, first strand: chain 'i' and resid 76 through 78 Processing sheet with id=BA2, first strand: chain 'k' and resid 41 through 42 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: 5.487A pdb=" N ARG V 38 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 4.493A 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: 4.412A 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: 4.338A pdb=" N SER V 148 " --> pdb=" O THR V 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR V 160 " --> pdb=" O SER V 148 " (cutoff:3.500A) removed outlier: 7.242A 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: 4.501A 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: 6.864A 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: 4.358A 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: 7.096A 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: 6.174A 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: 3.957A 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: 3.961A 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: 5.119A pdb=" N VALDA 54 " --> pdb=" O ALADA 40 " (cutoff:3.500A) removed outlier: 6.924A 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: 5.118A 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: 5.118A 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: 3.652A 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: 16.334A 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: 3.862A 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: 5.899A 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: 16.334A 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: 3.852A pdb=" N GLYDC 56 " --> pdb=" O SERDC 38 " (cutoff:3.500A) removed outlier: 6.032A 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: 11.575A 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: 7.141A 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: 11.575A 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 101 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: 4.635A 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: 7.521A 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: 7.086A 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: 3.660A 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: 6.104A 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: 3.624A 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: 3.905A 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: 16.319A 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: 6.060A 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: 4.531A 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: 4.959A 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: 4.525A 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: 7.247A pdb=" N GLUDE 207 " --> pdb=" O THRDE 203 " (cutoff:3.500A) removed outlier: 7.528A 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: 3.808A 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: 3.716A 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: 3.600A 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: 3.752A pdb=" N THRDF 203 " --> pdb=" O GLUDF 207 " (cutoff:3.500A) removed outlier: 7.476A 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: 3.546A 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: 3.661A 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: 5.744A 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: 4.186A 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: 6.053A 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: 5.184A pdb=" N ARGDH 84 " --> pdb=" O THRDH 117 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALDH 333 " --> pdb=" O GLNDH 329 " (cutoff:3.500A) removed outlier: 3.821A 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: 3.714A 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: 6.769A pdb=" N ASNDH 157 " --> pdb=" O ILEDH 276 " (cutoff:3.500A) removed outlier: 5.996A 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: 4.259A 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: 3.642A pdb=" N SERDI 38 " --> pdb=" O GLYDI 56 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLYDI 56 " --> pdb=" O SERDI 38 " (cutoff:3.500A) removed outlier: 6.271A 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: 4.912A pdb=" N ARGDI 84 " --> pdb=" O THRDI 117 " (cutoff:3.500A) removed outlier: 6.412A 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: 4.912A 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: 3.516A 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: 7.283A pdb=" N SERDI 153 " --> pdb=" O THRDI 279 " (cutoff:3.500A) removed outlier: 4.507A 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: 5.121A 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: 3.969A 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: 7.695A pdb=" N SERDJ 153 " --> pdb=" O THRDJ 279 " (cutoff:3.500A) removed outlier: 5.431A 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: 3.698A 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: 7.971A 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: 3.698A pdb=" N PHEDK 82 " --> pdb=" O ALADK 318 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALADK 318 " --> pdb=" O PHEDK 82 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARGDK 84 " --> pdb=" O VALDK 316 " (cutoff:3.500A) removed outlier: 6.837A 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: 7.325A 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: 7.325A 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: 7.325A 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: 7.017A pdb=" N THRDK 117 " --> pdb=" O VALDK 316 " (cutoff:3.500A) removed outlier: 12.618A 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: 5.699A 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: 3.944A 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: 7.233A pdb=" N ASNDK 157 " --> pdb=" O ILEDK 276 " (cutoff:3.500A) removed outlier: 6.021A 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: 7.083A pdb=" N GLUDK 207 " --> pdb=" O THRDK 203 " (cutoff:3.500A) removed outlier: 3.906A 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) 5424 hydrogen bonds defined for protein. 15312 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: 68.81 Time building geometry restraints manager: 36.70 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: 20218 1.30 - 1.43: 26646 1.43 - 1.55: 68285 1.55 - 1.68: 0 1.68 - 1.81: 911 Bond restraints: 116060 Sorted by residual: bond pdb=" CA SERDJ 350 " pdb=" CB SERDJ 350 " ideal model delta sigma weight residual 1.538 1.481 0.057 1.22e-02 6.72e+03 2.16e+01 bond pdb=" C ASN S 202 " pdb=" O ASN S 202 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.14e-02 7.69e+03 2.07e+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 ... (remaining 116055 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.56: 3080 106.56 - 114.01: 67610 114.01 - 121.45: 57445 121.45 - 128.89: 29442 128.89 - 136.33: 284 Bond angle restraints: 157861 Sorted by residual: angle pdb=" C GLNDJ 383 " pdb=" CA GLNDJ 383 " pdb=" CB GLNDJ 383 " ideal model delta sigma weight residual 110.88 99.12 11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" CA ASN S 202 " pdb=" CB ASN S 202 " pdb=" CG ASN S 202 " ideal model delta sigma weight residual 112.60 105.74 6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" C THRCD 42 " pdb=" N GLNCD 43 " pdb=" CA GLNCD 43 " ideal model delta sigma weight residual 121.54 133.90 -12.36 1.91e+00 2.74e-01 4.19e+01 angle pdb=" C ASNDI 270 " pdb=" N THRDI 271 " pdb=" CA THRDI 271 " ideal model delta sigma weight residual 122.27 110.41 11.86 1.85e+00 2.92e-01 4.11e+01 angle pdb=" N GLN K 59 " pdb=" CA GLN K 59 " pdb=" CB GLN K 59 " ideal model delta sigma weight residual 111.00 102.76 8.24 1.33e+00 5.65e-01 3.84e+01 ... (remaining 157856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 66626 17.98 - 35.96: 2744 35.96 - 53.94: 468 53.94 - 71.93: 69 71.93 - 89.91: 51 Dihedral angle restraints: 69958 sinusoidal: 26275 harmonic: 43683 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 -107.15 -15.45 0 2.50e+00 1.60e-01 3.82e+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 -136.44 13.84 0 2.50e+00 1.60e-01 3.07e+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 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 ... (remaining 69955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 17524 0.085 - 0.169: 1216 0.169 - 0.254: 6 0.254 - 0.339: 2 0.339 - 0.424: 4 Chirality restraints: 18752 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 4.48e+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 4.17e+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 3.69e+00 ... (remaining 18749 not shown) Planarity restraints: 20962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYRDK 382 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C TYRDK 382 " 0.060 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 7.86e+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=" CB ASN S 202 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" CG ASN S 202 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN S 202 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN S 202 " -0.016 2.00e-02 2.50e+03 ... (remaining 20959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1627 2.63 - 3.20: 108786 3.20 - 3.77: 173777 3.77 - 4.33: 228417 4.33 - 4.90: 387484 Nonbonded interactions: 900091 Sorted by model distance: nonbonded pdb=" O GLN K 59 " pdb=" NE2 GLN K 59 " model vdw 2.066 2.520 nonbonded pdb=" O MET y 138 " pdb=" OG1 THR y 142 " model vdw 2.109 2.440 nonbonded pdb=" O METCF 138 " pdb=" OG1 THRCF 142 " model vdw 2.143 2.440 nonbonded pdb=" O ILEDA 156 " pdb=" OG SERDA 266 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR c 55 " pdb=" OG SER f 26 " model vdw 2.156 2.440 ... (remaining 900086 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 'CA' selection = chain 'CB' selection = chain 'CC' selection = chain 'CD' } ncs_group { reference = chain 'CF' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.110 Extract box with map and model: 28.110 Check model and map are aligned: 1.210 Set scattering table: 0.730 Process input model: 247.440 Find NCS groups from input model: 6.890 Set up NCS constraints: 1.160 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 293.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 116060 Z= 0.198 Angle : 0.499 14.739 157861 Z= 0.273 Chirality : 0.040 0.424 18752 Planarity : 0.003 0.041 20962 Dihedral : 10.457 89.908 41906 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 1.97 % Allowed : 6.77 % Favored : 91.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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 (0.07), residues: 15116 helix: 3.00 (0.08), residues: 4777 sheet: -0.50 (0.09), residues: 3017 loop : -0.44 (0.07), residues: 7322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2033 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1788 time to evaluate : 9.223 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 outliers start: 245 outliers final: 126 residues processed: 1988 average time/residue: 0.9561 time to fit residues: 3290.9941 Evaluate side-chains 1466 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1340 time to evaluate : 9.214 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 0.7582 time to fit residues: 196.4239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1273 optimal weight: 3.9990 chunk 1142 optimal weight: 0.7980 chunk 634 optimal weight: 6.9990 chunk 390 optimal weight: 4.9990 chunk 771 optimal weight: 0.4980 chunk 610 optimal weight: 9.9990 chunk 1181 optimal weight: 10.0000 chunk 457 optimal weight: 0.6980 chunk 718 optimal weight: 0.9980 chunk 879 optimal weight: 6.9990 chunk 1369 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN D 180 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 GLN ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN J 255 GLN J 259 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 GLN P 37 GLN P 90 ASN P 121 GLN Q 135 GLN R 16 GLN S 67 GLN T 104 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN a 116 GLN b 19 GLN ** c 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 GLN ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 120 ASN l 132 ASN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN i 120 ASN n 132 ASN V 90 ASN W 169 GLN W 255 GLN X 28 ASN X 85 ASN q 49 GLN q 97 GLN ** r 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 83 GLN v 90 ASN ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 197 ASN ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 26 ASN ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 385 ASN DC 268 GLN ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 338 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 319 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 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 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** CE 242 HIS ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 71 ASN ** z 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN z 160 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 116060 Z= 0.186 Angle : 0.544 11.984 157861 Z= 0.280 Chirality : 0.041 0.206 18752 Planarity : 0.003 0.044 20962 Dihedral : 3.563 23.436 16071 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.25 % Favored : 95.74 % Rotamer: Outliers : 1.95 % Allowed : 11.18 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.94 (0.07), residues: 15116 helix: 3.01 (0.07), residues: 4817 sheet: -0.49 (0.09), residues: 2892 loop : -0.52 (0.07), residues: 7407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1468 time to evaluate : 9.256 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 outliers start: 242 outliers final: 103 residues processed: 1628 average time/residue: 0.9389 time to fit residues: 2692.9098 Evaluate side-chains 1434 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1331 time to evaluate : 9.357 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.7870 time to fit residues: 166.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 761 optimal weight: 0.9980 chunk 425 optimal weight: 4.9990 chunk 1139 optimal weight: 9.9990 chunk 932 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 1371 optimal weight: 10.0000 chunk 1482 optimal weight: 7.9990 chunk 1221 optimal weight: 1.9990 chunk 1360 optimal weight: 4.9990 chunk 467 optimal weight: 6.9990 chunk 1100 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN M 85 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN b 19 GLN ** c 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 GLN ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 115 ASN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN ** i 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN W 47 GLN X 90 ASN X 252 GLN q 97 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 97 GLN ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 83 GLN ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 381 ASN DB 89 ASN ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DD 23 ASN ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 213 HIS ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 280 ASN ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 129 GLN ** DI 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 310 GLN DJ 314 GLN ** DJ 352 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** ** CE 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 83 ASN w 76 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 116060 Z= 0.256 Angle : 0.552 12.054 157861 Z= 0.283 Chirality : 0.041 0.187 18752 Planarity : 0.003 0.049 20962 Dihedral : 3.707 24.572 16071 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.62 % Favored : 95.37 % Rotamer: Outliers : 1.81 % Allowed : 12.52 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.80 (0.07), residues: 15116 helix: 2.86 (0.07), residues: 4853 sheet: -0.56 (0.09), residues: 2904 loop : -0.60 (0.07), residues: 7359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1378 time to evaluate : 9.357 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 outliers start: 225 outliers final: 96 residues processed: 1566 average time/residue: 0.9210 time to fit residues: 2548.7749 Evaluate side-chains 1385 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1289 time to evaluate : 9.181 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.7577 time to fit residues: 152.0491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1355 optimal weight: 0.4980 chunk 1031 optimal weight: 6.9990 chunk 711 optimal weight: 0.0470 chunk 151 optimal weight: 2.9990 chunk 654 optimal weight: 10.0000 chunk 921 optimal weight: 20.0000 chunk 1376 optimal weight: 0.9980 chunk 1457 optimal weight: 9.9990 chunk 719 optimal weight: 4.9990 chunk 1304 optimal weight: 4.9990 chunk 392 optimal weight: 5.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN M 190 ASN Q 135 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 240 ASN 5 324 ASN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN k 13 GLN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 ASN X 67 GLN q 97 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 26 ASN ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 401 ASN ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 129 GLN ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 213 HIS ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 83 ASN ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 116060 Z= 0.205 Angle : 0.542 12.063 157861 Z= 0.276 Chirality : 0.040 0.199 18752 Planarity : 0.003 0.050 20962 Dihedral : 3.692 23.891 16071 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.48 % Favored : 95.51 % Rotamer: Outliers : 1.48 % Allowed : 13.86 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.81 (0.07), residues: 15116 helix: 2.90 (0.07), residues: 4829 sheet: -0.60 (0.09), residues: 2879 loop : -0.58 (0.07), residues: 7408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1397 time to evaluate : 9.235 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: 184 outliers final: 95 residues processed: 1537 average time/residue: 0.9345 time to fit residues: 2525.2588 Evaluate side-chains 1401 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1306 time to evaluate : 9.242 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.7649 time to fit residues: 151.7974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1213 optimal weight: 3.9990 chunk 827 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 1085 optimal weight: 6.9990 chunk 601 optimal weight: 9.9990 chunk 1243 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 744 optimal weight: 5.9990 chunk 1308 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN C 67 GLN E 47 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN M 259 GLN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN Q 135 GLN R 37 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN e 230 GLN 5 324 ASN j 17 GLN m 29 ASN ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 HIS V 90 ASN X 28 ASN ** X 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 97 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 26 ASN DB 89 ASN ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 385 ASN DC 268 GLN ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 280 ASN DG 401 ASN ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 213 HIS ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 119 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 116060 Z= 0.421 Angle : 0.649 12.391 157861 Z= 0.335 Chirality : 0.043 0.215 18752 Planarity : 0.004 0.054 20962 Dihedral : 4.147 24.007 16071 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.82 % Favored : 94.17 % Rotamer: Outliers : 2.03 % Allowed : 14.99 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.44 (0.07), residues: 15116 helix: 2.47 (0.07), residues: 4871 sheet: -0.71 (0.09), residues: 2860 loop : -0.79 (0.07), residues: 7385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1558 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1305 time to evaluate : 9.572 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: 253 outliers final: 151 residues processed: 1493 average time/residue: 0.9310 time to fit residues: 2459.1176 Evaluate side-chains 1402 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1251 time to evaluate : 9.343 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 0 residues processed: 151 average time/residue: 0.7837 time to fit residues: 236.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 490 optimal weight: 2.9990 chunk 1312 optimal weight: 0.1980 chunk 288 optimal weight: 1.9990 chunk 855 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 1459 optimal weight: 5.9990 chunk 1211 optimal weight: 7.9990 chunk 675 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 482 optimal weight: 2.9990 chunk 765 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 GLN K 237 GLN M 190 ASN ** M 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN Q 135 GLN R 37 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN a 240 ASN 5 324 ASN 9 318 ASN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN k 32 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN X 85 ASN r 55 GLN t 69 ASN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 323 ASN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 401 ASN ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 213 HIS ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 89 GLN CE 182 ASN ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 114 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 116060 Z= 0.194 Angle : 0.562 12.246 157861 Z= 0.286 Chirality : 0.041 0.227 18752 Planarity : 0.003 0.053 20962 Dihedral : 3.884 24.047 16071 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.49 % Favored : 95.50 % Rotamer: Outliers : 1.16 % Allowed : 15.87 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 15116 helix: 2.76 (0.07), residues: 4852 sheet: -0.67 (0.09), residues: 2838 loop : -0.71 (0.07), residues: 7426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1354 time to evaluate : 9.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 78 residues processed: 1448 average time/residue: 0.9325 time to fit residues: 2380.0943 Evaluate side-chains 1363 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1285 time to evaluate : 8.282 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.6898 time to fit residues: 114.3494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1406 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 831 optimal weight: 5.9990 chunk 1065 optimal weight: 4.9990 chunk 825 optimal weight: 1.9990 chunk 1228 optimal weight: 0.9990 chunk 814 optimal weight: 4.9990 chunk 1453 optimal weight: 0.6980 chunk 909 optimal weight: 6.9990 chunk 886 optimal weight: 0.9990 chunk 671 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN L 85 ASN ** M 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN N 67 GLN Q 135 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN b 19 GLN ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN X 67 GLN X 252 GLN ** r 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 55 GLN u 83 GLN ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 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 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 401 ASN DH 197 ASN ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 194 HIS ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 213 HIS ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 71 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 116060 Z= 0.168 Angle : 0.557 13.274 157861 Z= 0.280 Chirality : 0.040 0.229 18752 Planarity : 0.003 0.055 20962 Dihedral : 3.737 24.142 16071 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.62 % Favored : 95.36 % Rotamer: Outliers : 0.76 % Allowed : 16.77 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.77 (0.07), residues: 15116 helix: 2.94 (0.08), residues: 4813 sheet: -0.65 (0.09), residues: 2914 loop : -0.64 (0.07), residues: 7389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1375 time to evaluate : 9.269 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: 94 outliers final: 49 residues processed: 1434 average time/residue: 0.9473 time to fit residues: 2381.3732 Evaluate side-chains 1334 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1285 time to evaluate : 9.259 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.7920 time to fit residues: 85.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 899 optimal weight: 8.9990 chunk 580 optimal weight: 5.9990 chunk 868 optimal weight: 3.9990 chunk 437 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 924 optimal weight: 30.0000 chunk 990 optimal weight: 6.9990 chunk 718 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 chunk 1142 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN ** H 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 318 ASN j 17 GLN ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 ASN V 28 ASN X 28 ASN X 67 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 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 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 83 ASN ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 71 ASN CF 119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 116060 Z= 0.207 Angle : 0.581 13.067 157861 Z= 0.292 Chirality : 0.041 0.234 18752 Planarity : 0.003 0.056 20962 Dihedral : 3.756 24.146 16071 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.36 % Rotamer: Outliers : 0.68 % Allowed : 17.54 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.75 (0.07), residues: 15116 helix: 2.90 (0.08), residues: 4797 sheet: -0.64 (0.09), residues: 2877 loop : -0.64 (0.07), residues: 7442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1326 time to evaluate : 9.344 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: 84 outliers final: 46 residues processed: 1374 average time/residue: 0.9433 time to fit residues: 2279.3105 Evaluate side-chains 1334 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1288 time to evaluate : 9.290 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.7778 time to fit residues: 80.6720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 1322 optimal weight: 3.9990 chunk 1392 optimal weight: 0.5980 chunk 1270 optimal weight: 3.9990 chunk 1354 optimal weight: 7.9990 chunk 815 optimal weight: 0.6980 chunk 590 optimal weight: 5.9990 chunk 1063 optimal weight: 1.9990 chunk 415 optimal weight: 0.9990 chunk 1223 optimal weight: 0.0870 chunk 1281 optimal weight: 40.0000 chunk 1349 optimal weight: 0.7980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN ** N 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN T 104 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN 9 318 ASN ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN X 67 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 83 GLN ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 268 GLN DC 401 ASN ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DD 319 ASN ** DE 107 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 401 ASN ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 71 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 116060 Z= 0.151 Angle : 0.580 17.278 157861 Z= 0.288 Chirality : 0.040 0.258 18752 Planarity : 0.003 0.053 20962 Dihedral : 3.615 24.707 16071 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 0.41 % Allowed : 17.77 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 15116 helix: 3.00 (0.08), residues: 4801 sheet: -0.56 (0.09), residues: 2870 loop : -0.58 (0.07), residues: 7445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1402 time to evaluate : 9.328 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: 51 outliers final: 16 residues processed: 1437 average time/residue: 0.9511 time to fit residues: 2394.6741 Evaluate side-chains 1319 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1303 time to evaluate : 9.220 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.8376 time to fit residues: 36.9517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 889 optimal weight: 1.9990 chunk 1432 optimal weight: 20.0000 chunk 874 optimal weight: 9.9990 chunk 679 optimal weight: 4.9990 chunk 995 optimal weight: 4.9990 chunk 1502 optimal weight: 3.9990 chunk 1382 optimal weight: 0.5980 chunk 1196 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 924 optimal weight: 30.0000 chunk 733 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 GLN N 174 ASN ** N 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 104 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN d 19 GLN d 25 ASN 9 318 ASN ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN X 67 GLN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 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 401 ASN ** DH 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 129 GLN DI 190 GLN DI 274 ASN ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 116060 Z= 0.250 Angle : 0.613 15.401 157861 Z= 0.307 Chirality : 0.041 0.227 18752 Planarity : 0.003 0.059 20962 Dihedral : 3.737 25.380 16071 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 0.32 % Allowed : 18.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 0.77 (0.07), residues: 15116 helix: 2.82 (0.08), residues: 4828 sheet: -0.51 (0.10), residues: 2737 loop : -0.63 (0.07), residues: 7551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30232 Ramachandran restraints generated. 15116 Oldfield, 0 Emsley, 15116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1306 time to evaluate : 9.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 1323 average time/residue: 0.9445 time to fit residues: 2199.6661 Evaluate side-chains 1296 residues out of total 12435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1273 time to evaluate : 8.246 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7100 time to fit residues: 41.9545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1508 random chunks: chunk 950 optimal weight: 9.9990 chunk 1274 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 1103 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 332 optimal weight: 5.9990 chunk 1198 optimal weight: 0.9990 chunk 501 optimal weight: 0.9990 chunk 1230 optimal weight: 6.9990 chunk 151 optimal weight: 0.0170 chunk 220 optimal weight: 0.0000 overall best weight: 0.4826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN B 235 GLN D 16 GLN ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN T 104 GLN ** T 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 243 ASN a 18 GLN d 19 GLN 9 318 ASN ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 132 ASN i 104 ASN ** k 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 ASN X 67 GLN X 90 ASN ** t 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 155 GLN ** DF 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DG 401 ASN ** DH 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DH 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.104459 restraints weight = 328995.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103808 restraints weight = 183895.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.104328 restraints weight = 123233.345| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 116060 Z= 0.154 Angle : 0.598 16.999 157861 Z= 0.296 Chirality : 0.041 0.256 18752 Planarity : 0.003 0.053 20962 Dihedral : 3.592 25.176 16071 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.90 % Favored : 96.09 % Rotamer: Outliers : 0.19 % Allowed : 18.49 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.01 % 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: 15116 helix: 2.96 (0.08), residues: 4813 sheet: -0.48 (0.10), residues: 2801 loop : -0.56 (0.07), residues: 7502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33700.27 seconds wall clock time: 585 minutes 54.36 seconds (35154.36 seconds total)