Starting phenix.real_space_refine (version: dev) on Thu Dec 22 12:03:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/12_2022/7dr7_30825.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 185": "NH1" <-> "NH2" Residue "U TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 185": "NH1" <-> "NH2" Residue "X PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "Y TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 185": "NH1" <-> "NH2" Residue "1 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 123": "NH1" <-> "NH2" Residue "1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48304 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "B" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "D" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "E" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "F" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1804 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "G" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "I" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1593 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "J" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "L" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "M" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "O" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "P" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "Q" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "R" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "S" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "T" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "U" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "V" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1682 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "W" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1499 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "X" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "1" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "2" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Time building chain proxies: 24.68, per 1000 atoms: 0.51 Number of scatterers: 48304 At special positions: 0 Unit cell: (193.746, 175.294, 139.708, 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 308 16.00 O 9189 8.00 N 8276 7.00 C 30531 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: 17.33 Conformation dependent library (CDL) restraints added in 6.6 seconds 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11450 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 73 sheets defined 38.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.575A pdb=" N VAL A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 98 removed outlier: 3.698A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.760A pdb=" N THR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.992A pdb=" N LYS A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.619A pdb=" N TYR A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.759A pdb=" N GLU B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.519A pdb=" N SER B 63 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 103 removed outlier: 3.788A pdb=" N ALA B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.556A pdb=" N ASN B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.687A pdb=" N SER B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 3.719A pdb=" N GLN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.963A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.550A pdb=" N ALA C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 99 removed outlier: 3.910A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.603A pdb=" N SER C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 removed outlier: 4.100A pdb=" N THR C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.350A pdb=" N ALA C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.551A pdb=" N VAL C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.755A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.677A pdb=" N SER D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.702A pdb=" N ASP D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 180 removed outlier: 3.528A pdb=" N GLU D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 179 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 4.237A pdb=" N LYS D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.644A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 34 removed outlier: 3.670A pdb=" N LYS E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 105 removed outlier: 3.520A pdb=" N LYS E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.670A pdb=" N VAL E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 removed outlier: 3.693A pdb=" N LYS E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 207 removed outlier: 3.509A pdb=" N VAL E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.691A pdb=" N HIS E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.584A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 79 through 102 removed outlier: 3.569A pdb=" N TYR F 83 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL F 85 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 86 " --> pdb=" O ASP F 82 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS F 92 " --> pdb=" O HIS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.563A pdb=" N TYR F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 178 removed outlier: 3.564A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.501A pdb=" N GLU F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 18 through 30 removed outlier: 3.529A pdb=" N HIS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 102 removed outlier: 3.526A pdb=" N ALA G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN G 84 " --> pdb=" O THR G 80 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 92 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 124 removed outlier: 3.660A pdb=" N ASP G 116 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.661A pdb=" N MET G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.675A pdb=" N ALA G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 246 removed outlier: 3.581A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 78 removed outlier: 3.630A pdb=" N GLN H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 97 removed outlier: 3.592A pdb=" N SER H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 154 removed outlier: 3.922A pdb=" N GLY H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 177 removed outlier: 3.961A pdb=" N ARG H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 72 removed outlier: 4.411A pdb=" N VAL I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 94 removed outlier: 3.557A pdb=" N ARG I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 147 removed outlier: 4.183A pdb=" N LEU I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER I 141 " --> pdb=" O PHE I 137 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 removed outlier: 3.571A pdb=" N GLU I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 108 removed outlier: 3.716A pdb=" N LYS J 101 " --> pdb=" O GLU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 Processing helix chain 'J' and resid 169 through 181 Proline residue: J 175 - end of helix Processing helix chain 'J' and resid 195 through 214 removed outlier: 3.975A pdb=" N ARG J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 123 removed outlier: 3.847A pdb=" N LEU K 122 " --> pdb=" O ASP K 118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 147 Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.570A pdb=" N VAL K 198 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 225 Processing helix chain 'K' and resid 255 through 261 removed outlier: 4.114A pdb=" N MET K 259 " --> pdb=" O ASP K 255 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER K 261 " --> pdb=" O ALA K 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 34 removed outlier: 3.669A pdb=" N LYS L 30 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 105 removed outlier: 3.520A pdb=" N LYS L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 120 through 128 removed outlier: 3.670A pdb=" N VAL L 124 " --> pdb=" O ASP L 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 186 removed outlier: 3.693A pdb=" N LYS L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS L 185 " --> pdb=" O LYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 207 removed outlier: 3.509A pdb=" N VAL L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 231 through 240 removed outlier: 3.691A pdb=" N HIS L 238 " --> pdb=" O GLU L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 244 Processing helix chain 'M' and resid 19 through 29 removed outlier: 3.583A pdb=" N ALA M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'M' and resid 79 through 102 removed outlier: 3.569A pdb=" N TYR M 83 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG M 84 " --> pdb=" O GLY M 80 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL M 85 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU M 86 " --> pdb=" O ASP M 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS M 92 " --> pdb=" O HIS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 121 removed outlier: 3.562A pdb=" N TYR M 121 " --> pdb=" O VAL M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 178 removed outlier: 3.504A pdb=" N PHE M 173 " --> pdb=" O ASN M 169 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS M 176 " --> pdb=" O THR M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 removed outlier: 3.534A pdb=" N GLU M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 230 Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 18 through 30 removed outlier: 3.529A pdb=" N HIS N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 102 removed outlier: 3.525A pdb=" N ALA N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN N 84 " --> pdb=" O THR N 80 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU N 92 " --> pdb=" O ASN N 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN N 95 " --> pdb=" O ARG N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 124 removed outlier: 3.660A pdb=" N ASP N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 179 removed outlier: 3.662A pdb=" N MET N 174 " --> pdb=" O ALA N 170 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 201 removed outlier: 3.676A pdb=" N ALA N 191 " --> pdb=" O LYS N 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS N 195 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS N 199 " --> pdb=" O LYS N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 246 removed outlier: 3.623A pdb=" N GLU N 243 " --> pdb=" O LYS N 239 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA N 245 " --> pdb=" O GLU N 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 28 removed outlier: 3.575A pdb=" N VAL O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 98 removed outlier: 3.697A pdb=" N ALA O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL O 89 " --> pdb=" O ASN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 121 removed outlier: 3.761A pdb=" N THR O 119 " --> pdb=" O LYS O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 176 removed outlier: 3.992A pdb=" N LYS O 174 " --> pdb=" O GLU O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 195 Processing helix chain 'O' and resid 196 through 198 No H-bonds generated for 'chain 'O' and resid 196 through 198' Processing helix chain 'O' and resid 221 through 230 removed outlier: 3.619A pdb=" N TYR O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.759A pdb=" N GLU P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS P 32 " --> pdb=" O ILE P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.519A pdb=" N SER P 63 " --> pdb=" O GLU P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 103 removed outlier: 3.788A pdb=" N ALA P 85 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS P 86 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU P 88 " --> pdb=" O ASP P 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 118 removed outlier: 3.555A pdb=" N ASN P 118 " --> pdb=" O GLN P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 185 removed outlier: 3.687A pdb=" N SER P 180 " --> pdb=" O GLY P 176 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 206 removed outlier: 3.721A pdb=" N GLN P 204 " --> pdb=" O ILE P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 238 removed outlier: 3.963A pdb=" N GLU P 236 " --> pdb=" O GLU P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 241 No H-bonds generated for 'chain 'P' and resid 239 through 241' Processing helix chain 'Q' and resid 19 through 31 removed outlier: 3.550A pdb=" N ALA Q 28 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Q 30 " --> pdb=" O MET Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 99 removed outlier: 3.910A pdb=" N LEU Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 116 removed outlier: 3.603A pdb=" N SER Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 122 removed outlier: 4.100A pdb=" N THR Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 4.349A pdb=" N ALA Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS Q 175 " --> pdb=" O TYR Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 179 Processing helix chain 'Q' and resid 183 through 199 removed outlier: 3.551A pdb=" N VAL Q 188 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU Q 197 " --> pdb=" O ARG Q 193 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 234 Processing helix chain 'R' and resid 21 through 33 removed outlier: 3.754A pdb=" N VAL R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 103 removed outlier: 3.677A pdb=" N SER R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.704A pdb=" N ASP R 114 " --> pdb=" O LYS R 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 180 removed outlier: 3.528A pdb=" N GLU R 176 " --> pdb=" O ALA R 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU R 178 " --> pdb=" O LYS R 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU R 180 " --> pdb=" O GLU R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 202 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 243 removed outlier: 3.643A pdb=" N TYR R 239 " --> pdb=" O GLU R 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 78 removed outlier: 3.629A pdb=" N GLN S 61 " --> pdb=" O ALA S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 97 removed outlier: 3.592A pdb=" N SER S 89 " --> pdb=" O TYR S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 154 removed outlier: 4.114A pdb=" N GLY S 148 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER S 152 " --> pdb=" O GLY S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 177 removed outlier: 3.961A pdb=" N ARG S 177 " --> pdb=" O ASN S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 4.412A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 94 removed outlier: 3.557A pdb=" N ARG T 86 " --> pdb=" O ASN T 82 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU T 92 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER T 94 " --> pdb=" O ASP T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 147 removed outlier: 4.184A pdb=" N LEU T 138 " --> pdb=" O TYR T 134 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 165 removed outlier: 3.571A pdb=" N GLU T 158 " --> pdb=" O GLU T 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 108 removed outlier: 3.716A pdb=" N LYS U 101 " --> pdb=" O GLU U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 126 Processing helix chain 'U' and resid 169 through 181 Proline residue: U 175 - end of helix Processing helix chain 'U' and resid 195 through 214 removed outlier: 3.979A pdb=" N ARG U 201 " --> pdb=" O ASP U 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 123 removed outlier: 3.848A pdb=" N LEU V 122 " --> pdb=" O ASP V 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY V 123 " --> pdb=" O GLU V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 147 Processing helix chain 'V' and resid 191 through 202 removed outlier: 3.570A pdb=" N VAL V 198 " --> pdb=" O LEU V 194 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS V 201 " --> pdb=" O GLU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 225 Processing helix chain 'V' and resid 255 through 262 removed outlier: 4.114A pdb=" N MET V 259 " --> pdb=" O ASP V 255 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER V 261 " --> pdb=" O ALA V 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 91 Processing helix chain 'W' and resid 95 through 110 Processing helix chain 'W' and resid 135 through 138 Processing helix chain 'W' and resid 151 through 155 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 167 through 186 removed outlier: 3.788A pdb=" N LYS W 184 " --> pdb=" O ALA W 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG W 185 " --> pdb=" O LEU W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 110 removed outlier: 3.642A pdb=" N THR X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR X 95 " --> pdb=" O ALA X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 129 removed outlier: 3.681A pdb=" N VAL X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG X 120 " --> pdb=" O ALA X 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR X 129 " --> pdb=" O THR X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 181 removed outlier: 3.650A pdb=" N ALA X 175 " --> pdb=" O ASP X 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP X 179 " --> pdb=" O ALA X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 203 removed outlier: 4.708A pdb=" N GLU X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU X 194 " --> pdb=" O ALA X 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.528A pdb=" N ARG Y 129 " --> pdb=" O LEU Y 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Y 136 " --> pdb=" O ALA Y 132 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 161 removed outlier: 3.518A pdb=" N LEU Y 155 " --> pdb=" O ALA Y 151 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN Y 161 " --> pdb=" O ASN Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 212 removed outlier: 3.690A pdb=" N GLY Y 209 " --> pdb=" O SER Y 205 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL Y 210 " --> pdb=" O HIS Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 239 removed outlier: 3.620A pdb=" N LEU Y 227 " --> pdb=" O GLU Y 223 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Y 238 " --> pdb=" O HIS Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 272 removed outlier: 3.575A pdb=" N HIS Y 269 " --> pdb=" O SER Y 265 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN Y 270 " --> pdb=" O ASP Y 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 91 Processing helix chain 'Z' and resid 95 through 110 Processing helix chain 'Z' and resid 135 through 138 Processing helix chain 'Z' and resid 150 through 154 removed outlier: 3.549A pdb=" N TYR Z 153 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 155 through 161 Processing helix chain 'Z' and resid 167 through 186 removed outlier: 3.788A pdb=" N LYS Z 184 " --> pdb=" O ALA Z 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG Z 185 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) Processing helix chain '1' and resid 92 through 110 Processing helix chain '1' and resid 114 through 129 removed outlier: 3.681A pdb=" N VAL 1 118 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG 1 120 " --> pdb=" O ALA 1 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 1 124 " --> pdb=" O ARG 1 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR 1 129 " --> pdb=" O THR 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 181 removed outlier: 3.649A pdb=" N ALA 1 175 " --> pdb=" O ASP 1 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 203 removed outlier: 4.697A pdb=" N GLU 1 192 " --> pdb=" O GLU 1 188 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU 1 193 " --> pdb=" O ALA 1 189 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU 1 194 " --> pdb=" O ALA 1 190 " (cutoff:3.500A) Processing helix chain '2' and resid 120 through 142 removed outlier: 3.528A pdb=" N ARG 2 129 " --> pdb=" O LEU 2 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 2 136 " --> pdb=" O ALA 2 132 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 162 removed outlier: 3.516A pdb=" N LEU 2 155 " --> pdb=" O ALA 2 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN 2 161 " --> pdb=" O ASN 2 157 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 212 removed outlier: 3.690A pdb=" N GLY 2 209 " --> pdb=" O SER 2 205 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL 2 210 " --> pdb=" O HIS 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 220 through 239 removed outlier: 3.620A pdb=" N LEU 2 227 " --> pdb=" O GLU 2 223 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 2 238 " --> pdb=" O HIS 2 234 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 272 removed outlier: 3.574A pdb=" N HIS 2 269 " --> pdb=" O SER 2 265 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN 2 270 " --> pdb=" O ASP 2 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.721A pdb=" N THR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 170 removed outlier: 4.887A pdb=" N GLN B 221 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.500A pdb=" N ALA B 140 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 153 " --> pdb=" O CYS B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.723A pdb=" N ILE C 212 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 67 removed outlier: 5.766A pdb=" N ILE C 63 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 74 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS C 65 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE C 72 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.567A pdb=" N PHE D 48 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 215 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 213 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 52 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA D 209 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.424A pdb=" N LEU D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL D 78 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN D 69 " --> pdb=" O MET D 76 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET D 76 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 139 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 168 through 169 removed outlier: 5.352A pdb=" N THR E 38 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 216 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 217 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 69 through 73 removed outlier: 6.435A pdb=" N LEU E 69 " --> pdb=" O MET E 80 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET E 80 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS E 71 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS E 78 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 162 removed outlier: 3.735A pdb=" N ASN F 214 " --> pdb=" O GLY F 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.670A pdb=" N LEU F 135 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 77 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN F 148 " --> pdb=" O PHE F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AB5, first strand: chain 'G' and resid 65 through 66 removed outlier: 3.664A pdb=" N LEU G 135 " --> pdb=" O SER G 75 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 136 through 140 removed outlier: 6.057A pdb=" N ALA H 10 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL H 185 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 28 through 30 removed outlier: 7.119A pdb=" N PHE H 28 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.569A pdb=" N LEU I 4 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.569A pdb=" N LEU I 4 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 21 through 23 removed outlier: 6.753A pdb=" N ALA I 21 " --> pdb=" O MET I 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'J' and resid 163 through 167 removed outlier: 5.691A pdb=" N THR J 39 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP J 54 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.814A pdb=" N GLU J 59 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 72 through 75 removed outlier: 6.653A pdb=" N THR J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN J 136 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL J 149 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 151 " --> pdb=" O GLN J 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN J 159 " --> pdb=" O SER J 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 181 through 182 removed outlier: 3.528A pdb=" N VAL K 66 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR K 238 " --> pdb=" O GLY K 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 73 through 75 removed outlier: 6.639A pdb=" N TYR K 75 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA K 79 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 87 through 90 removed outlier: 3.618A pdb=" N THR K 154 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 168 through 169 removed outlier: 5.350A pdb=" N THR L 38 " --> pdb=" O GLN L 53 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU L 216 " --> pdb=" O THR L 52 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL L 217 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 69 through 73 removed outlier: 6.435A pdb=" N LEU L 69 " --> pdb=" O MET L 80 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET L 80 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS L 71 " --> pdb=" O CYS L 78 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS L 78 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 160 through 162 removed outlier: 3.735A pdb=" N ASN M 214 " --> pdb=" O GLY M 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 66 through 67 removed outlier: 3.670A pdb=" N LEU M 135 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER M 77 " --> pdb=" O SER M 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN M 148 " --> pdb=" O PHE M 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 161 through 164 Processing sheet with id=AD6, first strand: chain 'N' and resid 65 through 66 removed outlier: 3.664A pdb=" N LEU N 135 " --> pdb=" O SER N 75 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY N 144 " --> pdb=" O ASP N 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 158 through 161 Processing sheet with id=AD8, first strand: chain 'O' and resid 63 through 64 removed outlier: 3.722A pdb=" N THR O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 167 through 170 removed outlier: 4.888A pdb=" N GLN P 221 " --> pdb=" O ASN P 225 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN P 225 " --> pdb=" O GLN P 221 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 78 through 80 removed outlier: 3.500A pdb=" N ALA P 140 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU P 153 " --> pdb=" O CYS P 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 158 through 161 removed outlier: 3.723A pdb=" N ILE Q 212 " --> pdb=" O TYR Q 224 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 63 through 67 removed outlier: 5.765A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE Q 74 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS Q 65 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE Q 72 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.566A pdb=" N PHE R 48 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 215 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU R 213 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 52 " --> pdb=" O GLU R 211 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA R 209 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.424A pdb=" N LEU R 67 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL R 78 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN R 69 " --> pdb=" O MET R 76 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET R 76 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY R 139 " --> pdb=" O GLY R 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 136 through 140 removed outlier: 6.057A pdb=" N ALA S 10 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL S 185 " --> pdb=" O LEU S 200 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 28 through 30 removed outlier: 7.118A pdb=" N PHE S 28 " --> pdb=" O VAL S 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 42 through 44 Processing sheet with id=AE9, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.570A pdb=" N LEU T 4 " --> pdb=" O HIS T 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.570A pdb=" N LEU T 4 " --> pdb=" O HIS T 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 21 through 23 removed outlier: 6.753A pdb=" N ALA T 21 " --> pdb=" O MET T 28 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 35 through 37 Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 167 removed outlier: 5.692A pdb=" N THR U 39 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP U 54 " --> pdb=" O THR U 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 57 through 59 removed outlier: 6.815A pdb=" N GLU U 59 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE U 63 " --> pdb=" O GLU U 59 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 72 through 75 removed outlier: 6.653A pdb=" N THR U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN U 136 " --> pdb=" O PHE U 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL U 149 " --> pdb=" O ASP U 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER U 151 " --> pdb=" O GLN U 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN U 159 " --> pdb=" O SER U 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 181 through 182 removed outlier: 3.511A pdb=" N VAL V 66 " --> pdb=" O LEU V 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR V 238 " --> pdb=" O GLY V 241 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 87 through 90 removed outlier: 3.618A pdb=" N THR V 154 " --> pdb=" O SER V 99 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 144 through 147 Processing sheet with id=AG1, first strand: chain 'W' and resid 40 through 42 removed outlier: 6.241A pdb=" N ALA W 42 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 54 through 58 removed outlier: 6.579A pdb=" N ILE W 61 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 163 through 167 removed outlier: 5.877A pdb=" N THR X 41 " --> pdb=" O ASP X 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL X 212 " --> pdb=" O ALA X 227 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA X 227 " --> pdb=" O VAL X 212 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 59 through 60 removed outlier: 3.634A pdb=" N ASP X 67 " --> pdb=" O ALA X 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 73 through 77 removed outlier: 3.674A pdb=" N CYS X 82 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE X 80 " --> pdb=" O ILE X 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP X 143 " --> pdb=" O GLY X 146 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 197 through 201 removed outlier: 5.794A pdb=" N THR Y 74 " --> pdb=" O ASP Y 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU Y 260 " --> pdb=" O MET Y 248 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS Y 250 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS Y 258 " --> pdb=" O HIS Y 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 92 through 94 removed outlier: 3.852A pdb=" N ALA Y 92 " --> pdb=" O THR Y 100 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA Y 94 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 107 through 108 Processing sheet with id=AG9, first strand: chain 'Y' and resid 118 through 119 Processing sheet with id=AH1, first strand: chain 'Z' and resid 144 through 147 Processing sheet with id=AH2, first strand: chain 'Z' and resid 40 through 42 removed outlier: 6.242A pdb=" N ALA Z 42 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 54 through 56 Processing sheet with id=AH4, first strand: chain '1' and resid 163 through 167 removed outlier: 5.877A pdb=" N THR 1 41 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL 1 212 " --> pdb=" O ALA 1 227 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA 1 227 " --> pdb=" O VAL 1 212 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '1' and resid 59 through 60 removed outlier: 3.633A pdb=" N ASP 1 67 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '1' and resid 73 through 77 removed outlier: 3.673A pdb=" N CYS 1 82 " --> pdb=" O HIS 1 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 1 80 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP 1 143 " --> pdb=" O GLY 1 146 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 197 through 201 removed outlier: 5.794A pdb=" N THR 2 74 " --> pdb=" O ASP 2 89 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU 2 260 " --> pdb=" O MET 2 248 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS 2 250 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS 2 258 " --> pdb=" O HIS 2 250 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 92 through 94 removed outlier: 3.853A pdb=" N ALA 2 92 " --> pdb=" O THR 2 100 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA 2 94 " --> pdb=" O ILE 2 98 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE 2 98 " --> pdb=" O ALA 2 94 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 107 through 108 Processing sheet with id=AI1, first strand: chain '2' and resid 118 through 119 2405 hydrogen bonds defined for protein. 6780 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: 18.67 Time building geometry restraints manager: 18.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15943 1.34 - 1.46: 6999 1.46 - 1.57: 25734 1.57 - 1.69: 0 1.69 - 1.81: 508 Bond restraints: 49184 Sorted by residual: bond pdb=" C PHE G 61 " pdb=" N SER G 62 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.33e-02 5.65e+03 6.12e+00 bond pdb=" C PHE G 60 " pdb=" N PHE G 61 " ideal model delta sigma weight residual 1.327 1.305 0.022 9.40e-03 1.13e+04 5.57e+00 bond pdb=" C PHE N 60 " pdb=" N PHE N 61 " ideal model delta sigma weight residual 1.332 1.361 -0.028 1.40e-02 5.10e+03 4.11e+00 bond pdb=" N ARG N 4 " pdb=" CA ARG N 4 " ideal model delta sigma weight residual 1.459 1.438 0.021 1.21e-02 6.83e+03 3.13e+00 bond pdb=" N PHE G 61 " pdb=" CA PHE G 61 " ideal model delta sigma weight residual 1.458 1.430 0.028 1.61e-02 3.86e+03 3.07e+00 ... (remaining 49179 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 1083 106.15 - 113.12: 26621 113.12 - 120.10: 16985 120.10 - 127.07: 21373 127.07 - 134.05: 400 Bond angle restraints: 66462 Sorted by residual: angle pdb=" N ARG I 145 " pdb=" CA ARG I 145 " pdb=" C ARG I 145 " ideal model delta sigma weight residual 112.23 120.27 -8.04 1.26e+00 6.30e-01 4.07e+01 angle pdb=" N ARG X 123 " pdb=" CA ARG X 123 " pdb=" C ARG X 123 " ideal model delta sigma weight residual 111.36 117.47 -6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N ARG G 3 " pdb=" CA ARG G 3 " pdb=" C ARG G 3 " ideal model delta sigma weight residual 111.28 105.22 6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N GLU X 236 " pdb=" CA GLU X 236 " pdb=" C GLU X 236 " ideal model delta sigma weight residual 110.42 118.52 -8.10 1.46e+00 4.69e-01 3.07e+01 angle pdb=" N ARG G 8 " pdb=" CA ARG G 8 " pdb=" C ARG G 8 " ideal model delta sigma weight residual 111.28 118.75 -7.47 1.35e+00 5.49e-01 3.07e+01 ... (remaining 66457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 28862 16.20 - 32.40: 565 32.40 - 48.60: 199 48.60 - 64.80: 28 64.80 - 81.00: 10 Dihedral angle restraints: 29664 sinusoidal: 11730 harmonic: 17934 Sorted by residual: dihedral pdb=" CA ILE Z 154 " pdb=" C ILE Z 154 " pdb=" N TYR Z 155 " pdb=" CA TYR Z 155 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLN O 200 " pdb=" C GLN O 200 " pdb=" N SER O 201 " pdb=" CA SER O 201 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLN A 200 " pdb=" C GLN A 200 " pdb=" N SER A 201 " pdb=" CA SER A 201 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 29661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6513 0.066 - 0.132: 915 0.132 - 0.198: 21 0.198 - 0.264: 2 0.264 - 0.330: 4 Chirality restraints: 7455 Sorted by residual: chirality pdb=" CA ARG I 145 " pdb=" N ARG I 145 " pdb=" C ARG I 145 " pdb=" CB ARG I 145 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG G 8 " pdb=" N ARG G 8 " pdb=" C ARG G 8 " pdb=" CB ARG G 8 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA ARG N 3 " pdb=" N ARG N 3 " pdb=" C ARG N 3 " pdb=" CB ARG N 3 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 7452 not shown) Planarity restraints: 8575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 101 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO H 102 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS X 233 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO X 234 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO X 234 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO X 234 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER N 2 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C SER N 2 " -0.045 2.00e-02 2.50e+03 pdb=" O SER N 2 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG N 3 " 0.015 2.00e-02 2.50e+03 ... (remaining 8572 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1311 2.70 - 3.25: 47577 3.25 - 3.80: 73632 3.80 - 4.35: 99276 4.35 - 4.90: 168382 Nonbonded interactions: 390178 Sorted by model distance: nonbonded pdb=" O ARG B 10 " pdb=" O GLY B 11 " model vdw 2.151 3.040 nonbonded pdb=" NH2 ARG A 81 " pdb=" O GLY G 154 " model vdw 2.198 2.520 nonbonded pdb=" OG1 THR O 31 " pdb=" O ARG O 163 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR A 31 " pdb=" O ARG A 163 " model vdw 2.211 2.440 nonbonded pdb=" O LYS 2 79 " pdb=" OH TYR 2 215 " model vdw 2.211 2.440 ... (remaining 390173 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 '1' selection = chain 'X' } ncs_group { reference = chain '2' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = (chain 'E' and resid 2 through 244) selection = chain 'L' } ncs_group { reference = (chain 'F' and resid 4 through 232) selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 1 through 197) selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = (chain 'K' and resid 47 through 261) selection = (chain 'V' and resid 47 through 261) } ncs_group { reference = chain 'W' selection = (chain 'Z' and (resid 21 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 308 5.16 5 C 30531 2.51 5 N 8276 2.21 5 O 9189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.410 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.410 Process input model: 112.160 Find NCS groups from input model: 5.010 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 49184 Z= 0.244 Angle : 0.612 8.238 66462 Z= 0.373 Chirality : 0.044 0.330 7455 Planarity : 0.004 0.072 8575 Dihedral : 8.328 81.000 18214 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.09), residues: 6164 helix: -3.18 (0.07), residues: 2162 sheet: -1.35 (0.11), residues: 1458 loop : -1.04 (0.11), residues: 2544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2281 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2266 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 2274 average time/residue: 0.6995 time to fit residues: 2515.9170 Evaluate side-chains 1376 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1369 time to evaluate : 6.005 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.8283 time to fit residues: 16.7262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 514 optimal weight: 6.9990 chunk 461 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 477 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 553 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 227 HIS C 43 HIS ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN D 171 GLN D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 52 GLN F 88 HIS ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN G 40 ASN G 100 GLN G 102 GLN G 142 HIS G 230 GLN G 235 GLN H 33 GLN I 8 GLN I 168 GLN I 193 ASN J 159 GLN J 180 GLN K 83 ASN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN K 202 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 109 GLN M 207 ASN N 100 GLN N 142 HIS N 235 GLN N 240 HIS O 94 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN P 227 HIS Q 43 HIS R 121 HIS R 144 ASN R 171 GLN R 181 GLN S 162 HIS T 8 GLN T 110 HIS T 168 GLN T 193 ASN U 159 GLN U 174 GLN U 180 GLN ** V 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 GLN V 126 HIS V 149 ASN V 192 GLN W 58 HIS W 105 ASN W 117 HIS X 105 HIS Y 247 ASN Z 58 HIS Z 105 ASN Z 205 HIS 1 105 HIS 2 104 ASN 2 196 ASN 2 234 HIS 2 247 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 49184 Z= 0.321 Angle : 0.662 11.566 66462 Z= 0.354 Chirality : 0.046 0.205 7455 Planarity : 0.005 0.078 8575 Dihedral : 4.998 33.489 6827 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 6164 helix: -0.99 (0.10), residues: 2238 sheet: -0.86 (0.12), residues: 1470 loop : -0.96 (0.12), residues: 2456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1415 time to evaluate : 6.012 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: 165 outliers final: 106 residues processed: 1501 average time/residue: 0.6034 time to fit residues: 1477.5567 Evaluate side-chains 1313 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1207 time to evaluate : 5.583 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.4199 time to fit residues: 92.0143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 307 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 460 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 554 optimal weight: 0.7980 chunk 598 optimal weight: 0.8980 chunk 493 optimal weight: 4.9990 chunk 549 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 444 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN B 186 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN I 87 ASN J 159 GLN J 180 GLN K 114 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 178 GLN R 69 ASN R 181 GLN T 8 GLN T 27 GLN T 87 ASN U 180 GLN V 202 GLN X 74 HIS Y 96 ASN Y 247 ASN Z 117 HIS 1 74 HIS 1 130 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 49184 Z= 0.212 Angle : 0.576 9.335 66462 Z= 0.305 Chirality : 0.044 0.171 7455 Planarity : 0.004 0.048 8575 Dihedral : 4.732 29.913 6827 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.10), residues: 6164 helix: 0.15 (0.11), residues: 2231 sheet: -0.51 (0.12), residues: 1486 loop : -0.81 (0.12), residues: 2447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1336 time to evaluate : 5.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 43 residues processed: 1379 average time/residue: 0.6140 time to fit residues: 1402.6556 Evaluate side-chains 1217 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1174 time to evaluate : 6.621 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4449 time to fit residues: 43.4306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 547 optimal weight: 3.9990 chunk 416 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 chunk 556 optimal weight: 3.9990 chunk 588 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 526 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 96 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 GLN J 180 GLN K 126 HIS L 75 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 GLN Q 175 HIS R 181 GLN T 8 GLN V 149 ASN Y 247 ASN Z 117 HIS Z 125 GLN 2 82 HIS 2 96 ASN 2 247 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.083 49184 Z= 0.430 Angle : 0.663 10.453 66462 Z= 0.348 Chirality : 0.047 0.179 7455 Planarity : 0.005 0.050 8575 Dihedral : 5.002 32.166 6827 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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 (0.10), residues: 6164 helix: 0.18 (0.11), residues: 2252 sheet: -0.55 (0.12), residues: 1473 loop : -0.95 (0.12), residues: 2439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1212 time to evaluate : 5.506 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: 171 outliers final: 104 residues processed: 1287 average time/residue: 0.5941 time to fit residues: 1270.9146 Evaluate side-chains 1247 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1143 time to evaluate : 5.534 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 0.4184 time to fit residues: 90.2945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 490 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 438 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 502 optimal weight: 0.7980 chunk 406 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 528 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 193 ASN J 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 ASN P 211 ASN R 69 ASN R 181 GLN R 222 ASN U 107 ASN W 125 GLN Y 96 ASN Y 247 ASN Z 125 GLN 2 96 ASN 2 247 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 49184 Z= 0.210 Angle : 0.558 8.986 66462 Z= 0.295 Chirality : 0.043 0.188 7455 Planarity : 0.004 0.049 8575 Dihedral : 4.689 28.757 6827 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.14 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 6164 helix: 0.65 (0.11), residues: 2241 sheet: -0.36 (0.13), residues: 1462 loop : -0.85 (0.12), residues: 2461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1225 time to evaluate : 5.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 42 residues processed: 1272 average time/residue: 0.6001 time to fit residues: 1267.3349 Evaluate side-chains 1183 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1141 time to evaluate : 5.282 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4174 time to fit residues: 40.2778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 198 optimal weight: 0.9980 chunk 530 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 345 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 589 optimal weight: 5.9990 chunk 489 optimal weight: 0.2980 chunk 272 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 309 optimal weight: 0.3980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 96 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN J 159 GLN L 33 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 181 GLN W 125 GLN 2 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 49184 Z= 0.274 Angle : 0.581 9.733 66462 Z= 0.305 Chirality : 0.044 0.178 7455 Planarity : 0.004 0.053 8575 Dihedral : 4.697 28.974 6827 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.10), residues: 6164 helix: 0.72 (0.11), residues: 2248 sheet: -0.37 (0.13), residues: 1466 loop : -0.86 (0.12), residues: 2450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1179 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 45 residues processed: 1216 average time/residue: 0.6196 time to fit residues: 1255.5433 Evaluate side-chains 1191 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1146 time to evaluate : 5.447 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4432 time to fit residues: 45.9963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 568 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 335 optimal weight: 7.9990 chunk 430 optimal weight: 8.9990 chunk 333 optimal weight: 0.9980 chunk 496 optimal weight: 5.9990 chunk 329 optimal weight: 0.0270 chunk 586 optimal weight: 8.9990 chunk 367 optimal weight: 0.0980 chunk 357 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 202 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 27 GLN J 159 GLN L 33 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 181 GLN W 125 GLN ** Y 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 49184 Z= 0.170 Angle : 0.541 8.673 66462 Z= 0.285 Chirality : 0.043 0.179 7455 Planarity : 0.004 0.051 8575 Dihedral : 4.520 29.901 6827 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 6164 helix: 0.99 (0.11), residues: 2240 sheet: -0.23 (0.13), residues: 1447 loop : -0.80 (0.12), residues: 2477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1215 time to evaluate : 5.390 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: 71 outliers final: 42 residues processed: 1240 average time/residue: 0.6290 time to fit residues: 1296.4183 Evaluate side-chains 1194 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1152 time to evaluate : 5.549 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4565 time to fit residues: 43.8449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 363 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 350 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 113 optimal weight: 0.8980 chunk 373 optimal weight: 0.9980 chunk 399 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 461 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 186 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN J 159 GLN L 33 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN W 125 GLN Y 247 ASN 2 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 49184 Z= 0.200 Angle : 0.550 11.159 66462 Z= 0.288 Chirality : 0.043 0.214 7455 Planarity : 0.004 0.054 8575 Dihedral : 4.482 30.180 6827 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.01 (0.11), residues: 6164 helix: 1.06 (0.11), residues: 2242 sheet: -0.24 (0.13), residues: 1459 loop : -0.75 (0.12), residues: 2463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1167 time to evaluate : 6.442 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: 48 outliers final: 27 residues processed: 1185 average time/residue: 0.6031 time to fit residues: 1184.3347 Evaluate side-chains 1167 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1140 time to evaluate : 6.536 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5490 time to fit residues: 36.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 533 optimal weight: 7.9990 chunk 562 optimal weight: 0.8980 chunk 513 optimal weight: 0.6980 chunk 546 optimal weight: 7.9990 chunk 329 optimal weight: 0.0040 chunk 238 optimal weight: 2.9990 chunk 429 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 494 optimal weight: 0.8980 chunk 517 optimal weight: 3.9990 chunk 545 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 8 ASN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN J 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 181 GLN W 125 GLN X 191 GLN Y 247 ASN ** Z 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 49184 Z= 0.172 Angle : 0.547 10.765 66462 Z= 0.285 Chirality : 0.043 0.253 7455 Planarity : 0.004 0.048 8575 Dihedral : 4.420 30.955 6827 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.90 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.11 (0.11), residues: 6164 helix: 1.17 (0.11), residues: 2240 sheet: -0.22 (0.13), residues: 1464 loop : -0.67 (0.12), residues: 2460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1174 time to evaluate : 5.797 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: 29 outliers final: 17 residues processed: 1186 average time/residue: 0.6089 time to fit residues: 1194.0963 Evaluate side-chains 1139 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1122 time to evaluate : 5.538 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5089 time to fit residues: 25.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 359 optimal weight: 3.9990 chunk 578 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 606 optimal weight: 0.0570 chunk 558 optimal weight: 3.9990 chunk 483 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 373 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN J 159 GLN L 75 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 ASN ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 166 GLN R 181 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 ASN Y 247 ASN 2 237 HIS 2 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 49184 Z= 0.276 Angle : 0.599 11.645 66462 Z= 0.310 Chirality : 0.045 0.300 7455 Planarity : 0.004 0.056 8575 Dihedral : 4.572 30.759 6827 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.28 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.01 (0.11), residues: 6164 helix: 1.04 (0.11), residues: 2245 sheet: -0.26 (0.13), residues: 1469 loop : -0.72 (0.12), residues: 2450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1125 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 1142 average time/residue: 0.6202 time to fit residues: 1173.3280 Evaluate side-chains 1117 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1100 time to evaluate : 6.151 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4366 time to fit residues: 22.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 383 optimal weight: 0.3980 chunk 514 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 445 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 483 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 496 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN J 159 GLN L 75 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 GLN M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 181 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 ASN Z 101 ASN Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129049 restraints weight = 62315.151| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.10 r_work: 0.3367 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 49184 Z= 0.211 Angle : 0.577 11.163 66462 Z= 0.299 Chirality : 0.044 0.318 7455 Planarity : 0.004 0.056 8575 Dihedral : 4.518 31.247 6827 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.69 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.06 (0.11), residues: 6164 helix: 1.12 (0.11), residues: 2240 sheet: -0.21 (0.13), residues: 1469 loop : -0.71 (0.12), residues: 2455 =============================================================================== Job complete usr+sys time: 19137.42 seconds wall clock time: 337 minutes 53.76 seconds (20273.76 seconds total)