Starting phenix.real_space_refine on Fri Dec 8 15:22:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7php_13424/12_2023/7php_13424.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 41 5.16 5 C 5542 2.51 5 N 1440 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 85": "OE1" <-> "OE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "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: 8647 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3473 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 16, 'TRANS': 439} Chain breaks: 1 Chain: "H" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "N" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 5.28, per 1000 atoms: 0.61 Number of scatterers: 8647 At special positions: 0 Unit cell: (164.15, 135.34, 67.67, 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 41 16.00 O 1624 8.00 N 1440 7.00 C 5542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 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: 3.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 39.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 36 removed outlier: 4.243A pdb=" N GLU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Proline residue: A 17 - end of helix removed outlier: 3.618A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.716A pdb=" N ILE A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.897A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.759A pdb=" N LEU A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.139A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 108 removed outlier: 3.501A pdb=" N VAL A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 93 " --> pdb=" O HIS A 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Proline residue: A 101 - end of helix removed outlier: 3.521A pdb=" N ALA A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.687A pdb=" N ILE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 removed outlier: 4.629A pdb=" N LYS A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 153 removed outlier: 3.609A pdb=" N LEU A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 179 removed outlier: 4.186A pdb=" N MET A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 4.111A pdb=" N TRP A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 179 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 214 Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.908A pdb=" N ARG A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 3.576A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 removed outlier: 3.596A pdb=" N ALA A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 304 removed outlier: 3.511A pdb=" N MET A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 334 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.568A pdb=" N LEU A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 380 removed outlier: 4.481A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.575A pdb=" N HIS A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.675A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 445 removed outlier: 4.026A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.719A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.504A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'H' and resid 98 through 100c removed outlier: 3.828A pdb=" N HIS H 100b" --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER H 100d" --> pdb=" O GLN H 100 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N TRP H 100e" --> pdb=" O TYR H 100a" (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR H 100f" --> pdb=" O HIS H 100b" (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 100g" --> pdb=" O ALA H 100c" (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN H 100h" --> pdb=" O SER H 100d" (cutoff:3.500A) removed outlier: 10.572A pdb=" N GLY H 100i" --> pdb=" O TRP H 100e" (cutoff:3.500A) removed outlier: 10.135A pdb=" N GLY H 100j" --> pdb=" O TYR H 100f" (cutoff:3.500A) removed outlier: 10.895A pdb=" N LEU H 100k" --> pdb=" O TRP H 100g" (cutoff:3.500A) removed outlier: 9.473A pdb=" N ASP H 101 " --> pdb=" O ASN H 100h" (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR H 102 " --> pdb=" O GLY H 100i" (cutoff:3.500A) removed outlier: 9.639A pdb=" N TRP H 103 " --> pdb=" O GLY H 100j" (cutoff:3.500A) removed outlier: 8.805A pdb=" N GLY H 104 " --> pdb=" O LEU H 100k" (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLN H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N GLY H 106 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N THR H 107 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N LEU H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N VAL H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N THR H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N VAL H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N SER H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N SER H 113 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N SER H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N THR H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N GLY H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Proline residue: H 119 - end of helix removed outlier: 10.801A 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: 8.663A pdb=" N LYS H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER H 130 " --> pdb=" O PRO H 126 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY H 133 " --> pdb=" O LYS H 129 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N ALA H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N LEU H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N GLY H 139 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N CYS H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N LEU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N LYS H 143 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N ASP H 144 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N TYR H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N PHE H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Proline residue: H 147 - end of helix removed outlier: 9.224A pdb=" N VAL H 150 " --> pdb=" O PHE H 146 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR H 151 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N VAL H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) removed outlier: 11.779A pdb=" N SER H 153 " --> pdb=" O PRO H 149 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N TRP H 154 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N ASN H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLY H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 158 " --> pdb=" O TRP H 154 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N THR H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER H 161 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N GLY H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N THR H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N PHE H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 9.717A pdb=" N LEU H 170 " --> pdb=" O PHE H 166 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLN H 171 " --> pdb=" O PRO H 167 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N SER H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N SER H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY H 174 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N TYR H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N SER H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 11.722A pdb=" N LEU H 178 " --> pdb=" O GLY H 174 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N SER H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 11.613A pdb=" N SER H 180 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 11.949A pdb=" N VAL H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N VAL H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N THR H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N VAL H 184 " --> pdb=" O SER H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 8.551A pdb=" N SER H 188 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N TYR H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N ILE H 195 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N CYS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ASN H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N VAL H 198 " --> pdb=" O TYR H 194 " (cutoff:3.500A) removed outlier: 10.728A pdb=" N ASN H 199 " --> pdb=" O ILE H 195 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N HIS H 200 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N LYS H 201 " --> pdb=" O ASN H 197 " (cutoff:3.500A) Proline residue: H 202 - end of helix removed outlier: 5.074A pdb=" N THR H 205 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N LYS H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N VAL H 207 " --> pdb=" O SER H 203 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N ASP H 208 " --> pdb=" O ASN H 204 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N LYS H 209 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N LYS H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N VAL H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 10.689A 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 187 through 191 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.641A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.689A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.053A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.617A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.707A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.566A pdb=" N LEU H 124 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 6.051A 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: 3.566A pdb=" N LEU H 124 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 6.051A 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: 3.798A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.154A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.660A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.658A pdb=" N SER N 70 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'N' and resid 94 through 96 Sorry: Error in SS definitions, most likely atoms are absent for one of them.