Starting phenix.real_space_refine on Fri Dec 8 11:19:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pij_13438/12_2023/7pij_13438_neut.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5234 2.51 5 N 1368 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8194 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1678 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1582 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Chain: "B" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3064 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 12, 'TRANS': 385} Chain: "N" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 5.07, per 1000 atoms: 0.62 Number of scatterers: 8194 At special positions: 0 Unit cell: (124.08, 155.76, 99.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1560 8.00 N 1368 7.00 C 5234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.11 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.14 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG ACYS K 92 " distance=2.08 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG BCYS K 92 " distance=2.05 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: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 37.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.534A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 98 through 100c removed outlier: 3.770A pdb=" N ALA H 100c" --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N SER H 100d" --> pdb=" O GLN H 100 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP H 100e" --> pdb=" O TYR H 100a" (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR H 100f" --> pdb=" O HIS H 100b" (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP H 100g" --> pdb=" O ALA H 100c" (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN H 100h" --> pdb=" O SER H 100d" (cutoff:3.500A) removed outlier: 10.722A pdb=" N GLY H 100i" --> pdb=" O TRP H 100e" (cutoff:3.500A) removed outlier: 10.619A pdb=" N GLY H 100j" --> pdb=" O TYR H 100f" (cutoff:3.500A) removed outlier: 10.901A pdb=" N LEU H 100k" --> pdb=" O TRP H 100g" (cutoff:3.500A) removed outlier: 8.933A pdb=" N ASP H 101 " --> pdb=" O ASN H 100h" (cutoff:3.500A) removed outlier: 8.699A pdb=" N TYR H 102 " --> pdb=" O GLY H 100i" (cutoff:3.500A) removed outlier: 9.366A pdb=" N TRP H 103 " --> pdb=" O GLY H 100j" (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY H 104 " --> pdb=" O LEU H 100k" (cutoff:3.500A) removed outlier: 10.541A pdb=" N GLN H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N GLY H 106 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N THR H 107 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N LEU H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N VAL H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N THR H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N VAL H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N SER H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N SER H 113 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N SER H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N THR H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N GLY H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Proline residue: H 119 - end of helix removed outlier: 10.253A pdb=" N PHE H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Proline residue: H 123 - end of helix Proline residue: H 126 - end of helix removed outlier: 13.132A pdb=" N THR H 135 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA H 136 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA H 137 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N LEU H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N GLY H 139 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N CYS H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N LEU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N VAL H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N LYS H 143 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ASP H 144 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N TYR H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Proline residue: H 147 - end of helix removed outlier: 8.737A pdb=" N VAL H 150 " --> pdb=" O PHE H 146 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR H 151 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N VAL H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N SER H 153 " --> pdb=" O PRO H 149 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N TRP H 154 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ASN H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N SER H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER H 161 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N GLY H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N PHE H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 9.613A pdb=" N LEU H 170 " --> pdb=" O PHE H 166 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N GLN H 171 " --> pdb=" O PRO H 167 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N SER H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY H 174 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N SER H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N LEU H 178 " --> pdb=" O GLY H 174 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N SER H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 11.285A pdb=" N SER H 180 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N VAL H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N VAL H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N THR H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N VAL H 184 " --> pdb=" O SER H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 6.408A pdb=" N SER H 188 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N TYR H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 10.855A pdb=" N ILE H 195 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N CYS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N ASN H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N VAL H 198 " --> pdb=" O TYR H 194 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ASN H 199 " --> pdb=" O ILE H 195 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N HIS H 200 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N LYS H 201 " --> pdb=" O ASN H 197 " (cutoff:3.500A) Proline residue: H 202 - end of helix removed outlier: 5.070A pdb=" N THR H 205 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N LYS H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N VAL H 207 " --> pdb=" O SER H 203 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ASP H 208 " --> pdb=" O ASN H 204 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N LYS H 209 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N LYS H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N VAL H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLU H 212 " --> pdb=" O ASP H 208 " (cutoff:3.500A) Proline residue: H 213 - end of helix Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.538A pdb=" N SER L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 67 through 91 removed outlier: 3.569A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 105 through 139 Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.718A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 187 removed outlier: 4.066A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.739A pdb=" N THR B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.742A pdb=" N ASN B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.512A pdb=" N ILE B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.802A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 284 removed outlier: 3.828A pdb=" N ILE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.596A pdb=" N LEU B 307 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 347 removed outlier: 3.908A pdb=" N GLY B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 374 Proline residue: B 366 - end of helix Processing helix chain 'B' and resid 377 through 408 Proline residue: B 397 - end of helix Proline residue: B 402 - end of helix Processing helix chain 'B' and resid 417 through 437 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.897A pdb=" N ARG K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.570A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.696A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.900A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.900A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.541A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.521A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.655A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.710A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'N' and resid 17 through 21 removed outlier: 3.542A pdb=" N TYR N 79 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER N 70 " --> pdb=" O TYR N 79 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN N 81 " --> pdb=" O THR N 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.666A pdb=" N SER N 30 " --> pdb=" O ARG N 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 35 through 38 removed outlier: 3.848A pdb=" N GLY N 35 " --> pdb=" O ASN N 93 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR N 102 " --> pdb=" O ALA N 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 35 through 38 removed outlier: 3.848A pdb=" N GLY N 35 " --> pdb=" O ASN N 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 50 Processing sheet with id=AB9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.580A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 12 Sorry: Error in SS definitions, most likely atoms are absent for one of them.