Starting phenix.real_space_refine on Wed Mar 20 07:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gjq_9511/03_2024/5gjq_9511_updated.pdb" } resolution = 4.35 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= 0.006 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 490 5.16 5 C 62193 2.51 5 N 17067 2.21 5 O 18699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "a TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 150": "OE1" <-> "OE2" Residue "a GLU 151": "OE1" <-> "OE2" Residue "a GLU 185": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "b GLU 22": "OE1" <-> "OE2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b GLU 150": "OE1" <-> "OE2" Residue "b GLU 220": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "d TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "e GLU 148": "OE1" <-> "OE2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 116": "OE1" <-> "OE2" Residue "f PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "g TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g GLU 194": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "H ARG 336": "NH1" <-> "NH2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "h GLU 216": "OE1" <-> "OE2" Residue "h GLU 232": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I GLU 304": "OE1" <-> "OE2" Residue "I ARG 307": "NH1" <-> "NH2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "i GLU 2": "OE1" <-> "OE2" Residue "i GLU 48": "OE1" <-> "OE2" Residue "i GLU 65": "OE1" <-> "OE2" Residue "i TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 119": "OE1" <-> "OE2" Residue "i GLU 182": "OE1" <-> "OE2" Residue "i GLU 204": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 218": "OE1" <-> "OE2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J GLU 275": "OE1" <-> "OE2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J GLU 373": "OE1" <-> "OE2" Residue "j GLU 70": "OE1" <-> "OE2" Residue "j GLU 89": "OE1" <-> "OE2" Residue "j GLU 103": "OE1" <-> "OE2" Residue "j PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 232": "OE1" <-> "OE2" Residue "j GLU 241": "OE1" <-> "OE2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K GLU 189": "OE1" <-> "OE2" Residue "K ARG 287": "NH1" <-> "NH2" Residue "K GLU 291": "OE1" <-> "OE2" Residue "K GLU 332": "OE1" <-> "OE2" Residue "K GLU 381": "OE1" <-> "OE2" Residue "k GLU 173": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 217": "OE1" <-> "OE2" Residue "L GLU 234": "OE1" <-> "OE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L ARG 251": "NH1" <-> "NH2" Residue "L ARG 255": "NH1" <-> "NH2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L GLU 365": "OE1" <-> "OE2" Residue "l ARG 20": "NH1" <-> "NH2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l GLU 29": "OE1" <-> "OE2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ASP 127": "OD1" <-> "OD2" Residue "l GLU 232": "OE1" <-> "OE2" Residue "l GLU 235": "OE1" <-> "OE2" Residue "l GLU 236": "OE1" <-> "OE2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ARG 238": "NH1" <-> "NH2" Residue "M ARG 269": "NH1" <-> "NH2" Residue "M ARG 334": "NH1" <-> "NH2" Residue "M ARG 364": "NH1" <-> "NH2" Residue "M GLU 414": "OE1" <-> "OE2" Residue "m TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 197": "OE1" <-> "OE2" Residue "m GLU 202": "OE1" <-> "OE2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "n GLU 31": "OE1" <-> "OE2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 183": "OE1" <-> "OE2" Residue "n GLU 234": "OE1" <-> "OE2" Residue "n TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 294": "OE1" <-> "OE2" Residue "O GLU 364": "OE1" <-> "OE2" Residue "O GLU 368": "OE1" <-> "OE2" Residue "o GLU 145": "OE1" <-> "OE2" Residue "o GLU 150": "OE1" <-> "OE2" Residue "o GLU 151": "OE1" <-> "OE2" Residue "o GLU 185": "OE1" <-> "OE2" Residue "P PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 22": "OE1" <-> "OE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 139": "OE1" <-> "OE2" Residue "p GLU 150": "OE1" <-> "OE2" Residue "p GLU 220": "OE1" <-> "OE2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "Q GLU 332": "OE1" <-> "OE2" Residue "Q GLU 402": "OE1" <-> "OE2" Residue "q PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "r TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 49": "OE1" <-> "OE2" Residue "r TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s GLU 148": "OE1" <-> "OE2" Residue "s ASP 190": "OD1" <-> "OD2" Residue "s GLU 197": "OE1" <-> "OE2" Residue "t GLU 18": "OE1" <-> "OE2" Residue "t GLU 31": "OE1" <-> "OE2" Residue "t GLU 116": "OE1" <-> "OE2" Residue "U ARG 34": "NH1" <-> "NH2" Residue "U GLU 166": "OE1" <-> "OE2" Residue "U GLU 173": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "u GLU 194": "OE1" <-> "OE2" Residue "V GLU 236": "OE1" <-> "OE2" Residue "V GLU 247": "OE1" <-> "OE2" Residue "X GLU 31": "OE1" <-> "OE2" Residue "X GLU 183": "OE1" <-> "OE2" Residue "X GLU 234": "OE1" <-> "OE2" Residue "X TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 201": "OE1" <-> "OE2" Residue "x GLU 215": "OE1" <-> "OE2" Residue "x GLU 260": "OE1" <-> "OE2" Residue "x GLU 269": "OE1" <-> "OE2" Residue "y GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 98461 Number of models: 1 Model: "" Number of chains: 54 Chain: "a" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1845 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "b" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1707 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "c" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "d" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1724 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 236} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "e" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1766 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "g" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1672 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2879 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "h" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1853 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "I" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2720 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "i" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1744 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2820 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "j" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1913 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "k" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1691 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 236} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "L" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2860 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 356} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "l" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1726 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 7, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2858 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "m" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 5462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 5462 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 792} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 994 Unresolved non-hydrogen angles: 1352 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 28, 'HIS:plan': 12, 'PHE:plan': 14, 'GLU:plan': 33, 'ASP:plan': 26} Unresolved non-hydrogen planarities: 562 Chain: "n" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1873 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 237} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "O" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2372 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 10, 'PHE:plan': 10, 'GLU:plan': 20, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 405 Chain: "o" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 2828 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 406} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 554 Unresolved non-hydrogen angles: 720 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 17, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 310 Chain: "p" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2948 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 10, 'TRANS': 410} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 208 Chain: "q" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2767 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 368} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 207 Chain: "r" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2600 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 664 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 9, 'TYR:plan': 11, 'ASN:plan1': 9, 'ASP:plan': 12, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 417 Chain: "s" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1551 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1702 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 271 Chain: "t" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1644 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2131 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "u" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1678 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2011 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 248} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1300 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "X" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1873 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 237} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Y" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 308 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 12, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 150 Chain: "Z" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 3608 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 613} Link IDs: {'CIS': 2, 'PTRANS': 25, 'TRANS': 704} Chain breaks: 4 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 2133 Unresolved non-hydrogen angles: 2736 Unresolved non-hydrogen dihedrals: 1740 Unresolved non-hydrogen chiralities: 222 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 17, 'TYR:plan': 24, 'ASN:plan1': 37, 'TRP:plan': 5, 'ASP:plan': 37, 'PHE:plan': 22, 'GLU:plan': 55, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1113 Chain: "x" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2810 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "y" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 39.52, per 1000 atoms: 0.40 Number of scatterers: 98461 At special positions: 0 Unit cell: (319.93, 220.42, 215.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 490 16.00 P 12 15.00 O 18699 8.00 N 17067 7.00 C 62193 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.17 Conformation dependent library (CDL) restraints added in 15.0 seconds 26746 Ramachandran restraints generated. 13373 Oldfield, 0 Emsley, 13373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 485 helices and 103 sheets defined 44.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.38 Creating SS restraints... Processing helix chain 'a' and resid 49 through 70 Processing helix chain 'a' and resid 76 through 89 Processing helix chain 'a' and resid 130 through 142 removed outlier: 3.692A pdb=" N SER a 133 " --> pdb=" O SER a 130 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR a 136 " --> pdb=" O SER a 133 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY a 137 " --> pdb=" O TYR a 134 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR a 138 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL a 139 " --> pdb=" O TYR a 136 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR a 142 " --> pdb=" O VAL a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 166 Processing helix chain 'a' and resid 191 through 193 No H-bonds generated for 'chain 'a' and resid 191 through 193' Processing helix chain 'B' and resid 23 through 35 removed outlier: 4.059A pdb=" N ASN B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 84 through 105 Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.656A pdb=" N VAL B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.631A pdb=" N THR B 173 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU B 174 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 183 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'b' and resid 49 through 70 Processing helix chain 'b' and resid 76 through 90 Processing helix chain 'b' and resid 131 through 141 Processing helix chain 'b' and resid 148 through 165 Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.679A pdb=" N GLY C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 100 Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.764A pdb=" N TYR C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'c' and resid 4 through 7 No H-bonds generated for 'chain 'c' and resid 4 through 7' Processing helix chain 'c' and resid 57 through 77 Processing helix chain 'c' and resid 84 through 98 removed outlier: 4.366A pdb=" N LYS c 98 " --> pdb=" O LEU c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 153 removed outlier: 3.627A pdb=" N SER c 152 " --> pdb=" O GLY c 148 " (cutoff:3.500A) Processing helix chain 'c' and resid 160 through 177 removed outlier: 3.789A pdb=" N ARG c 177 " --> pdb=" O ASN c 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 removed outlier: 3.533A pdb=" N HIS D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.668A pdb=" N ILE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 178 Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'd' and resid 50 through 71 removed outlier: 4.608A pdb=" N VAL d 54 " --> pdb=" O ALA d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 90 Processing helix chain 'd' and resid 134 through 146 removed outlier: 5.160A pdb=" N LEU d 140 " --> pdb=" O PHE d 137 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER d 141 " --> pdb=" O LEU d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 153 through 170 Processing helix chain 'E' and resid 17 through 27 Processing helix chain 'E' and resid 56 through 59 Processing helix chain 'E' and resid 77 through 97 removed outlier: 3.589A pdb=" N ARG E 95 " --> pdb=" O CYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 184 through 197 removed outlier: 3.696A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'e' and resid 49 through 70 Processing helix chain 'e' and resid 76 through 90 removed outlier: 3.962A pdb=" N GLN e 89 " --> pdb=" O ASN e 85 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR e 90 " --> pdb=" O MET e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 142 removed outlier: 3.640A pdb=" N GLY e 137 " --> pdb=" O VAL e 133 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL e 138 " --> pdb=" O TYR e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 166 Processing helix chain 'e' and resid 192 through 200 removed outlier: 3.598A pdb=" N GLU e 197 " --> pdb=" O ALA e 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.652A pdb=" N LYS F 32 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 82 through 103 removed outlier: 4.171A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.905A pdb=" N LEU F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.502A pdb=" N VAL F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 231 through 240 removed outlier: 3.721A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 79 Processing helix chain 'f' and resid 85 through 99 removed outlier: 4.048A pdb=" N ARG f 99 " --> pdb=" O ILE f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 142 through 152 Proline residue: f 147 - end of helix Processing helix chain 'f' and resid 168 through 185 Processing helix chain 'G' and resid 20 through 30 removed outlier: 3.975A pdb=" N VAL G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 99 Processing helix chain 'G' and resid 105 through 120 removed outlier: 3.615A pdb=" N ILE G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 176 through 181 removed outlier: 4.067A pdb=" N MET G 180 " --> pdb=" O MET G 176 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 176 through 181' Processing helix chain 'G' and resid 184 through 198 removed outlier: 3.918A pdb=" N THR G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 233 No H-bonds generated for 'chain 'G' and resid 230 through 233' Processing helix chain 'g' and resid 57 through 77 removed outlier: 3.932A pdb=" N LEU g 77 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 101 Processing helix chain 'g' and resid 140 through 154 removed outlier: 5.674A pdb=" N ALA g 146 " --> pdb=" O ALA g 143 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN g 147 " --> pdb=" O TYR g 144 " (cutoff:3.500A) Proline residue: g 148 - end of helix removed outlier: 3.652A pdb=" N ARG g 151 " --> pdb=" O PRO g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 179 Processing helix chain 'g' and resid 210 through 213 Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.643A pdb=" N ASN H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 92 Proline residue: H 92 - end of helix Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.882A pdb=" N GLU H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 195 No H-bonds generated for 'chain 'H' and resid 192 through 195' Processing helix chain 'H' and resid 200 through 203 No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 222 through 229 Processing helix chain 'H' and resid 242 through 244 No H-bonds generated for 'chain 'H' and resid 242 through 244' Processing helix chain 'H' and resid 253 through 266 Processing helix chain 'H' and resid 277 through 280 No H-bonds generated for 'chain 'H' and resid 277 through 280' Processing helix chain 'H' and resid 293 through 306 Processing helix chain 'H' and resid 329 through 332 No H-bonds generated for 'chain 'H' and resid 329 through 332' Processing helix chain 'H' and resid 349 through 361 removed outlier: 4.524A pdb=" N SER H 361 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 376 Processing helix chain 'H' and resid 384 through 398 removed outlier: 4.085A pdb=" N GLY H 393 " --> pdb=" O CYS H 389 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET H 394 " --> pdb=" O THR H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 416 Processing helix chain 'H' and resid 419 through 421 No H-bonds generated for 'chain 'H' and resid 419 through 421' Processing helix chain 'h' and resid 23 through 35 removed outlier: 4.088A pdb=" N ASN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN h 34 " --> pdb=" O LYS h 30 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 105 Processing helix chain 'h' and resid 111 through 127 removed outlier: 3.675A pdb=" N VAL h 124 " --> pdb=" O ASP h 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR h 125 " --> pdb=" O ILE h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 183 Processing helix chain 'h' and resid 191 through 206 Processing helix chain 'h' and resid 232 through 240 Processing helix chain 'I' and resid 66 through 82 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 192 through 200 Processing helix chain 'I' and resid 202 through 205 No H-bonds generated for 'chain 'I' and resid 202 through 205' Processing helix chain 'I' and resid 232 through 242 Processing helix chain 'I' and resid 263 through 276 removed outlier: 3.780A pdb=" N VAL I 267 " --> pdb=" O GLY I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 290 Processing helix chain 'I' and resid 305 through 315 Processing helix chain 'I' and resid 339 through 342 No H-bonds generated for 'chain 'I' and resid 339 through 342' Processing helix chain 'I' and resid 360 through 369 Processing helix chain 'I' and resid 380 through 384 Processing helix chain 'I' and resid 394 through 409 removed outlier: 3.732A pdb=" N GLY I 403 " --> pdb=" O CYS I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'i' and resid 19 through 30 removed outlier: 3.655A pdb=" N GLY i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 100 Processing helix chain 'i' and resid 106 through 121 removed outlier: 3.675A pdb=" N TYR i 120 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR i 121 " --> pdb=" O MET i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 175 Processing helix chain 'i' and resid 183 through 194 Processing helix chain 'i' and resid 222 through 230 Processing helix chain 'J' and resid 25 through 59 removed outlier: 3.871A pdb=" N GLU J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 31 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LYS J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER J 39 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN J 53 " --> pdb=" O ARG J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'J' and resid 155 through 164 Processing helix chain 'J' and resid 166 through 170 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'J' and resid 197 through 206 removed outlier: 3.520A pdb=" N VAL J 203 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 223 Processing helix chain 'J' and resid 233 through 240 removed outlier: 3.536A pdb=" N MET J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 removed outlier: 3.875A pdb=" N LEU J 276 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 335 removed outlier: 3.639A pdb=" N LYS J 335 " --> pdb=" O ILE J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 358 through 372 Processing helix chain 'J' and resid 380 through 394 removed outlier: 3.995A pdb=" N ALA J 388 " --> pdb=" O GLU J 384 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 30 Processing helix chain 'j' and resid 80 through 101 Processing helix chain 'j' and resid 107 through 123 removed outlier: 3.643A pdb=" N ILE j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 178 Processing helix chain 'j' and resid 186 through 200 Processing helix chain 'j' and resid 208 through 210 No H-bonds generated for 'chain 'j' and resid 208 through 210' Processing helix chain 'j' and resid 230 through 247 removed outlier: 3.842A pdb=" N LYS j 246 " --> pdb=" O GLU j 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 82 removed outlier: 4.332A pdb=" N LYS K 45 " --> pdb=" O TYR K 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN K 48 " --> pdb=" O TYR K 44 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS K 74 " --> pdb=" O LYS K 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN K 76 " --> pdb=" O PHE K 72 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 180 Processing helix chain 'K' and resid 182 through 186 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 213 through 222 Processing helix chain 'K' and resid 242 through 257 Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.516A pdb=" N ARG K 287 " --> pdb=" O ARG K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 348 Processing helix chain 'K' and resid 361 through 365 Processing helix chain 'K' and resid 374 through 388 removed outlier: 3.920A pdb=" N GLY K 383 " --> pdb=" O CYS K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 406 Processing helix chain 'k' and resid 17 through 27 Processing helix chain 'k' and resid 56 through 59 Processing helix chain 'k' and resid 77 through 97 removed outlier: 3.545A pdb=" N ARG k 95 " --> pdb=" O CYS k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 119 Processing helix chain 'k' and resid 165 through 175 Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.712A pdb=" N GLU k 197 " --> pdb=" O LYS k 193 " (cutoff:3.500A) Processing helix chain 'k' and resid 222 through 235 Processing helix chain 'L' and resid 16 through 51 removed outlier: 3.564A pdb=" N HIS L 19 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY L 24 " --> pdb=" O GLU L 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 25 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS L 27 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG L 30 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN L 32 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU L 33 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU L 35 " --> pdb=" O GLN L 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU L 36 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS L 38 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN L 39 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS L 42 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER L 43 " --> pdb=" O TYR L 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 49 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 122 No H-bonds generated for 'chain 'L' and resid 119 through 122' Processing helix chain 'L' and resid 139 through 149 removed outlier: 3.550A pdb=" N ARG L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 154 No H-bonds generated for 'chain 'L' and resid 151 through 154' Processing helix chain 'L' and resid 159 through 161 No H-bonds generated for 'chain 'L' and resid 159 through 161' Processing helix chain 'L' and resid 181 through 190 removed outlier: 3.540A pdb=" N ARG L 185 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 225 removed outlier: 3.765A pdb=" N LEU L 214 " --> pdb=" O GLU L 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 215 " --> pdb=" O SER L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 239 No H-bonds generated for 'chain 'L' and resid 236 through 239' Processing helix chain 'L' and resid 250 through 264 removed outlier: 3.505A pdb=" N LEU L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU L 261 " --> pdb=" O LEU L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 284 No H-bonds generated for 'chain 'L' and resid 282 through 284' Processing helix chain 'L' and resid 287 through 290 No H-bonds generated for 'chain 'L' and resid 287 through 290' Processing helix chain 'L' and resid 306 through 316 removed outlier: 4.094A pdb=" N ILE L 315 " --> pdb=" O ASP L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 334 Processing helix chain 'L' and resid 341 through 355 Processing helix chain 'L' and resid 365 through 380 removed outlier: 3.668A pdb=" N LYS L 369 " --> pdb=" O GLU L 365 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA L 370 " --> pdb=" O ASP L 366 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS L 378 " --> pdb=" O VAL L 374 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU L 380 " --> pdb=" O ASP L 376 " (cutoff:3.500A) Processing helix chain 'l' and resid 22 through 31 Processing helix chain 'l' and resid 82 through 103 removed outlier: 4.104A pdb=" N THR l 87 " --> pdb=" O ALA l 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU l 88 " --> pdb=" O ASP l 84 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'l' and resid 110 through 118 WARNING: missing atoms! WARNING: missing atoms! Processing helix chain 'l' and resid 174 through 184 Processing helix chain 'l' and resid 195 through 205 Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.713A pdb=" N VAL l 237 " --> pdb=" O GLU l 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 83 removed outlier: 3.561A pdb=" N ILE M 54 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET M 55 " --> pdb=" O GLU M 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP M 71 " --> pdb=" O GLN M 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS M 74 " --> pdb=" O LYS M 70 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 175 removed outlier: 3.672A pdb=" N ALA M 174 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET M 175 " --> pdb=" O ARG M 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 170 through 175' Processing helix chain 'M' and resid 192 through 201 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'M' and resid 210 through 215 removed outlier: 3.566A pdb=" N LEU M 215 " --> pdb=" O LYS M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 243 Processing helix chain 'M' and resid 263 through 277 removed outlier: 3.860A pdb=" N LYS M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 290 No H-bonds generated for 'chain 'M' and resid 288 through 290' Processing helix chain 'M' and resid 305 through 317 Processing helix chain 'M' and resid 360 through 371 Processing helix chain 'M' and resid 381 through 387 Processing helix chain 'M' and resid 393 through 409 removed outlier: 3.678A pdb=" N LYS M 397 " --> pdb=" O GLY M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 427 Processing helix chain 'm' and resid 20 through 30 removed outlier: 3.930A pdb=" N VAL m 29 " --> pdb=" O ALA m 25 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS m 30 " --> pdb=" O MET m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 99 Processing helix chain 'm' and resid 105 through 120 removed outlier: 3.565A pdb=" N ILE m 118 " --> pdb=" O SER m 114 " (cutoff:3.500A) Proline residue: m 119 - end of helix Processing helix chain 'm' and resid 165 through 174 Processing helix chain 'm' and resid 176 through 181 removed outlier: 4.141A pdb=" N MET m 180 " --> pdb=" O MET m 176 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU m 181 " --> pdb=" O SER m 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 176 through 181' Processing helix chain 'm' and resid 184 through 198 removed outlier: 3.942A pdb=" N THR m 198 " --> pdb=" O ALA m 194 " (cutoff:3.500A) Processing helix chain 'm' and resid 230 through 233 No H-bonds generated for 'chain 'm' and resid 230 through 233' Processing helix chain 'N' and resid 6 through 13 removed outlier: 4.304A pdb=" N ASP N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 40 removed outlier: 4.334A pdb=" N ASN N 32 " --> pdb=" O ASN N 28 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA N 36 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU N 37 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU N 40 " --> pdb=" O ALA N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 49 Processing helix chain 'N' and resid 55 through 70 removed outlier: 3.992A pdb=" N GLN N 58 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 84 Processing helix chain 'N' and resid 95 through 118 removed outlier: 3.750A pdb=" N HIS N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR N 108 " --> pdb=" O CYS N 104 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR N 109 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS N 110 " --> pdb=" O ASP N 106 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 118 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 144 Processing helix chain 'N' and resid 147 through 157 removed outlier: 3.700A pdb=" N ILE N 153 " --> pdb=" O GLN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 170 Processing helix chain 'N' and resid 178 through 187 Processing helix chain 'N' and resid 191 through 206 Processing helix chain 'N' and resid 213 through 223 Processing helix chain 'N' and resid 226 through 238 Processing helix chain 'N' and resid 242 through 253 Processing helix chain 'N' and resid 258 through 271 removed outlier: 3.719A pdb=" N SER N 262 " --> pdb=" O GLN N 258 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER N 263 " --> pdb=" O GLN N 259 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL N 264 " --> pdb=" O PHE N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 330 Processing helix chain 'N' and resid 332 through 345 Processing helix chain 'N' and resid 350 through 357 Processing helix chain 'N' and resid 364 through 376 removed outlier: 3.684A pdb=" N ILE N 371 " --> pdb=" O THR N 367 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER N 374 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 384 through 388 Processing helix chain 'N' and resid 391 through 395 Processing helix chain 'N' and resid 398 through 411 removed outlier: 3.822A pdb=" N LEU N 408 " --> pdb=" O ALA N 404 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY N 409 " --> pdb=" O THR N 405 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL N 410 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE N 411 " --> pdb=" O SER N 407 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 426 removed outlier: 4.105A pdb=" N THR N 425 " --> pdb=" O GLN N 421 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR N 426 " --> pdb=" O LEU N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 450 removed outlier: 4.142A pdb=" N LEU N 443 " --> pdb=" O GLU N 439 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR N 444 " --> pdb=" O GLY N 440 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY N 447 " --> pdb=" O LEU N 443 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU N 448 " --> pdb=" O TYR N 444 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE N 449 " --> pdb=" O ALA N 445 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS N 450 " --> pdb=" O LEU N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 467 Processing helix chain 'N' and resid 471 through 485 removed outlier: 4.533A pdb=" N GLY N 477 " --> pdb=" O VAL N 473 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY N 482 " --> pdb=" O SER N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 502 Processing helix chain 'N' and resid 508 through 519 removed outlier: 3.713A pdb=" N ALA N 512 " --> pdb=" O THR N 508 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY N 517 " --> pdb=" O GLY N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 526 through 538 Processing helix chain 'N' and resid 543 through 555 removed outlier: 3.742A pdb=" N LEU N 548 " --> pdb=" O ILE N 544 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA N 549 " --> pdb=" O LEU N 545 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL N 550 " --> pdb=" O ARG N 546 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 572 removed outlier: 3.642A pdb=" N ALA N 565 " --> pdb=" O GLU N 562 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 590 removed outlier: 3.788A pdb=" N TYR N 584 " --> pdb=" O ARG N 580 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 608 Processing helix chain 'N' and resid 612 through 625 removed outlier: 3.998A pdb=" N GLY N 623 " --> pdb=" O VAL N 619 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE N 624 " --> pdb=" O GLU N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 removed outlier: 4.746A pdb=" N SER N 635 " --> pdb=" O GLU N 631 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU N 639 " --> pdb=" O SER N 635 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU N 640 " --> pdb=" O VAL N 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 646 through 659 removed outlier: 3.811A pdb=" N ALA N 653 " --> pdb=" O ARG N 649 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET N 654 " --> pdb=" O TYR N 650 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA N 655 " --> pdb=" O GLY N 651 " (cutoff:3.500A) Processing helix chain 'N' and resid 666 through 677 removed outlier: 3.738A pdb=" N LEU N 672 " --> pdb=" O ALA N 668 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU N 673 " --> pdb=" O ILE N 669 " (cutoff:3.500A) Proline residue: N 674 - end of helix Processing helix chain 'N' and resid 681 through 695 Processing helix chain 'N' and resid 704 through 718 Processing helix chain 'N' and resid 726 through 737 Processing helix chain 'N' and resid 757 through 767 removed outlier: 3.967A pdb=" N GLY N 762 " --> pdb=" O PRO N 758 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL N 763 " --> pdb=" O SER N 759 " (cutoff:3.500A) Processing helix chain 'N' and resid 776 through 780 Processing helix chain 'N' and resid 886 through 890 removed outlier: 3.571A pdb=" N LYS N 890 " --> pdb=" O PRO N 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 886 through 890' Processing helix chain 'N' and resid 934 through 938 Processing helix chain 'n' and resid 21 through 31 Processing helix chain 'n' and resid 81 through 102 Processing helix chain 'n' and resid 108 through 122 removed outlier: 3.908A pdb=" N TYR n 122 " --> pdb=" O TYR n 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 169 through 178 removed outlier: 3.979A pdb=" N LYS n 178 " --> pdb=" O THR n 174 " (cutoff:3.500A) Processing helix chain 'n' and resid 186 through 200 removed outlier: 4.527A pdb=" N LYS n 191 " --> pdb=" O ARG n 187 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU n 192 " --> pdb=" O ASP n 188 " (cutoff:3.500A) Processing helix chain 'n' and resid 218 through 220 No H-bonds generated for 'chain 'n' and resid 218 through 220' Processing helix chain 'n' and resid 229 through 242 Processing helix chain 'O' and resid 4 through 13 Processing helix chain 'O' and resid 16 through 31 removed outlier: 4.082A pdb=" N ALA O 20 " --> pdb=" O PRO O 16 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TRP O 22 " --> pdb=" O GLN O 18 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS O 23 " --> pdb=" O PRO O 19 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG O 24 " --> pdb=" O ALA O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 49 Proline residue: O 48 - end of helix Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.923A pdb=" N SER O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N HIS O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 86 removed outlier: 3.502A pdb=" N ILE O 79 " --> pdb=" O SER O 75 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN O 86 " --> pdb=" O HIS O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 109 through 124 Processing helix chain 'O' and resid 128 through 144 removed outlier: 3.572A pdb=" N GLU O 140 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 166 removed outlier: 3.608A pdb=" N LYS O 161 " --> pdb=" O ASP O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 181 Processing helix chain 'O' and resid 190 through 206 Processing helix chain 'O' and resid 214 through 217 No H-bonds generated for 'chain 'O' and resid 214 through 217' Processing helix chain 'O' and resid 222 through 225 No H-bonds generated for 'chain 'O' and resid 222 through 225' Processing helix chain 'O' and resid 231 through 241 Processing helix chain 'O' and resid 245 through 255 removed outlier: 3.695A pdb=" N THR O 253 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA O 254 " --> pdb=" O THR O 250 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP O 255 " --> pdb=" O LEU O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 262 No H-bonds generated for 'chain 'O' and resid 260 through 262' Processing helix chain 'O' and resid 265 through 283 Processing helix chain 'O' and resid 293 through 300 Processing helix chain 'O' and resid 306 through 316 Processing helix chain 'O' and resid 343 through 367 removed outlier: 3.627A pdb=" N LYS O 347 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY O 348 " --> pdb=" O GLN O 344 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET O 349 " --> pdb=" O GLN O 345 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL O 360 " --> pdb=" O TRP O 356 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 70 Processing helix chain 'o' and resid 76 through 89 Processing helix chain 'o' and resid 130 through 134 removed outlier: 3.646A pdb=" N SER o 133 " --> pdb=" O SER o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 136 through 142 Processing helix chain 'o' and resid 149 through 166 Processing helix chain 'o' and resid 191 through 193 No H-bonds generated for 'chain 'o' and resid 191 through 193' Processing helix chain 'P' and resid 6 through 23 removed outlier: 3.655A pdb=" N ARG P 12 " --> pdb=" O ARG P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 52 Processing helix chain 'P' and resid 57 through 76 removed outlier: 3.534A pdb=" N VAL P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 92 Processing helix chain 'P' and resid 100 through 108 removed outlier: 4.059A pdb=" N VAL P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN P 106 " --> pdb=" O ALA P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 131 removed outlier: 3.784A pdb=" N LEU P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 154 removed outlier: 3.858A pdb=" N ARG P 144 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR P 148 " --> pdb=" O ARG P 144 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 166 removed outlier: 3.645A pdb=" N LYS P 160 " --> pdb=" O GLY P 157 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA P 163 " --> pdb=" O LYS P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 196 Processing helix chain 'P' and resid 200 through 207 Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 217 through 237 removed outlier: 4.072A pdb=" N LEU P 224 " --> pdb=" O GLU P 220 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS P 225 " --> pdb=" O LYS P 221 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 252 Processing helix chain 'P' and resid 254 through 258 Processing helix chain 'P' and resid 260 through 276 removed outlier: 3.646A pdb=" N GLN P 264 " --> pdb=" O SER P 260 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN P 265 " --> pdb=" O GLU P 261 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA P 266 " --> pdb=" O LYS P 262 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER P 269 " --> pdb=" O GLN P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 removed outlier: 3.741A pdb=" N ASP P 285 " --> pdb=" O ASN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 297 No H-bonds generated for 'chain 'P' and resid 295 through 297' Processing helix chain 'P' and resid 301 through 310 Processing helix chain 'P' and resid 317 through 330 removed outlier: 5.094A pdb=" N MET P 326 " --> pdb=" O GLU P 322 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU P 327 " --> pdb=" O ASP P 323 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 369 removed outlier: 3.742A pdb=" N ARG P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS P 352 " --> pdb=" O GLU P 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP P 353 " --> pdb=" O LYS P 349 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA P 367 " --> pdb=" O ILE P 363 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS P 368 " --> pdb=" O ARG P 364 " (cutoff:3.500A) Processing helix chain 'P' and resid 376 through 381 Processing helix chain 'P' and resid 386 through 398 Processing helix chain 'P' and resid 421 through 452 removed outlier: 3.649A pdb=" N THR P 443 " --> pdb=" O VAL P 439 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS P 444 " --> pdb=" O ASN P 440 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU P 445 " --> pdb=" O LYS P 441 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE P 446 " --> pdb=" O THR P 442 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 70 Processing helix chain 'p' and resid 76 through 89 Processing helix chain 'p' and resid 131 through 141 Processing helix chain 'p' and resid 148 through 165 Processing helix chain 'Q' and resid 3 through 15 removed outlier: 3.647A pdb=" N VAL Q 7 " --> pdb=" O ALA Q 3 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU Q 8 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 31 removed outlier: 3.812A pdb=" N ASP Q 25 " --> pdb=" O GLU Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 58 Processing helix chain 'Q' and resid 62 through 77 removed outlier: 3.545A pdb=" N GLY Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU Q 70 " --> pdb=" O LEU Q 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 71 " --> pdb=" O GLY Q 67 " (cutoff:3.500A) Proline residue: Q 75 - end of helix Processing helix chain 'Q' and resid 82 through 88 Processing helix chain 'Q' and resid 93 through 97 removed outlier: 3.587A pdb=" N LEU Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 93 through 97' Processing helix chain 'Q' and resid 103 through 120 removed outlier: 3.987A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 140 removed outlier: 3.504A pdb=" N ALA Q 128 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 158 removed outlier: 5.512A pdb=" N ARG Q 155 " --> pdb=" O SER Q 151 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU Q 156 " --> pdb=" O GLN Q 152 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Q 157 " --> pdb=" O LEU Q 153 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS Q 158 " --> pdb=" O LEU Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 179 removed outlier: 3.736A pdb=" N THR Q 176 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 199 Processing helix chain 'Q' and resid 205 through 220 removed outlier: 3.960A pdb=" N SER Q 214 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 240 removed outlier: 3.942A pdb=" N TYR Q 231 " --> pdb=" O THR Q 227 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR Q 239 " --> pdb=" O ALA Q 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 4.295A pdb=" N LYS Q 252 " --> pdb=" O ILE Q 248 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR Q 253 " --> pdb=" O THR Q 249 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 270 Processing helix chain 'Q' and resid 284 through 295 Processing helix chain 'Q' and resid 300 through 307 Processing helix chain 'Q' and resid 310 through 313 No H-bonds generated for 'chain 'Q' and resid 310 through 313' Processing helix chain 'Q' and resid 319 through 338 Processing helix chain 'Q' and resid 347 through 354 Processing helix chain 'Q' and resid 358 through 370 removed outlier: 3.670A pdb=" N GLN Q 367 " --> pdb=" O ARG Q 363 " (cutoff:3.500A) Processing helix chain 'Q' and resid 395 through 421 removed outlier: 4.030A pdb=" N ASP Q 412 " --> pdb=" O SER Q 408 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Q 417 " --> pdb=" O SER Q 413 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS Q 420 " --> pdb=" O ASN Q 416 " (cutoff:3.500A) Processing helix chain 'q' and resid 57 through 77 Processing helix chain 'q' and resid 84 through 98 removed outlier: 4.474A pdb=" N LYS q 98 " --> pdb=" O LEU q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 143 through 153 removed outlier: 3.685A pdb=" N SER q 152 " --> pdb=" O GLY q 148 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 177 removed outlier: 3.732A pdb=" N ARG q 177 " --> pdb=" O ASN q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 36 through 46 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 67 through 92 Processing helix chain 'R' and resid 97 through 113 Processing helix chain 'R' and resid 117 through 131 removed outlier: 3.508A pdb=" N LYS R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 151 removed outlier: 3.566A pdb=" N GLY R 148 " --> pdb=" O LEU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 removed outlier: 4.269A pdb=" N ASN R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS R 163 " --> pdb=" O ARG R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 190 Processing helix chain 'R' and resid 195 through 204 removed outlier: 3.827A pdb=" N GLU R 199 " --> pdb=" O LYS R 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 230 Processing helix chain 'R' and resid 233 through 239 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.974A pdb=" N GLU R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 264 Processing helix chain 'R' and resid 268 through 282 removed outlier: 3.657A pdb=" N PHE R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN R 273 " --> pdb=" O SER R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 308 removed outlier: 4.151A pdb=" N TYR R 295 " --> pdb=" O TYR R 292 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL R 296 " --> pdb=" O ARG R 293 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG R 297 " --> pdb=" O TYR R 294 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS R 302 " --> pdb=" O MET R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 323 Processing helix chain 'R' and resid 327 through 338 removed outlier: 3.931A pdb=" N ARG R 336 " --> pdb=" O GLN R 332 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE R 337 " --> pdb=" O GLU R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 388 removed outlier: 3.523A pdb=" N VAL R 386 " --> pdb=" O LYS R 382 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 71 Processing helix chain 'r' and resid 77 through 90 Processing helix chain 'r' and resid 134 through 146 removed outlier: 5.291A pdb=" N LEU r 140 " --> pdb=" O PHE r 137 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER r 141 " --> pdb=" O LEU r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 153 through 170 Processing helix chain 'S' and resid 58 through 68 removed outlier: 3.655A pdb=" N ARG S 65 " --> pdb=" O HIS S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 87 removed outlier: 4.094A pdb=" N GLN S 81 " --> pdb=" O HIS S 78 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL S 86 " --> pdb=" O GLU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 100 removed outlier: 3.633A pdb=" N ARG S 96 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA S 97 " --> pdb=" O PHE S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 115 Processing helix chain 'S' and resid 161 through 178 removed outlier: 4.144A pdb=" N TYR S 166 " --> pdb=" O GLU S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 197 removed outlier: 3.745A pdb=" N GLN S 185 " --> pdb=" O TYR S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 202 through 217 removed outlier: 3.553A pdb=" N VAL S 206 " --> pdb=" O ALA S 202 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS S 210 " --> pdb=" O VAL S 206 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG S 216 " --> pdb=" O TYR S 212 " (cutoff:3.500A) Processing helix chain 'S' and resid 221 through 224 No H-bonds generated for 'chain 'S' and resid 221 through 224' Processing helix chain 'S' and resid 226 through 241 removed outlier: 3.865A pdb=" N PHE S 230 " --> pdb=" O VAL S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 244 through 260 Processing helix chain 'S' and resid 265 through 272 Processing helix chain 'S' and resid 282 through 298 Processing helix chain 'S' and resid 305 through 314 Processing helix chain 'S' and resid 322 through 338 Processing helix chain 'S' and resid 345 through 347 No H-bonds generated for 'chain 'S' and resid 345 through 347' Processing helix chain 'S' and resid 352 through 355 Processing helix chain 'S' and resid 358 through 369 removed outlier: 3.927A pdb=" N GLN S 365 " --> pdb=" O PHE S 361 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 366 " --> pdb=" O LEU S 362 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR S 369 " --> pdb=" O GLN S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 372 through 387 removed outlier: 5.190A pdb=" N GLU S 384 " --> pdb=" O ASP S 380 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS S 385 " --> pdb=" O GLN S 381 " (cutoff:3.500A) Processing helix chain 'S' and resid 391 through 397 removed outlier: 3.819A pdb=" N ARG S 397 " --> pdb=" O THR S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 399 through 412 removed outlier: 3.595A pdb=" N ILE S 403 " --> pdb=" O ARG S 399 " (cutoff:3.500A) Processing helix chain 'S' and resid 419 through 425 Processing helix chain 'S' and resid 431 through 443 removed outlier: 3.547A pdb=" N PHE S 436 " --> pdb=" O GLU S 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG S 443 " --> pdb=" O ALA S 439 " (cutoff:3.500A) Processing helix chain 'S' and resid 470 through 493 removed outlier: 3.605A pdb=" N SER S 490 " --> pdb=" O ILE S 486 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 70 Processing helix chain 's' and resid 76 through 90 removed outlier: 3.872A pdb=" N GLN s 89 " --> pdb=" O ASN s 85 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR s 90 " --> pdb=" O MET s 86 " (cutoff:3.500A) Processing helix chain 's' and resid 132 through 142 removed outlier: 3.665A pdb=" N GLY s 137 " --> pdb=" O VAL s 133 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL s 138 " --> pdb=" O TYR s 134 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG s 141 " --> pdb=" O GLY s 137 " (cutoff:3.500A) Processing helix chain 's' and resid 149 through 166 Processing helix chain 's' and resid 192 through 200 removed outlier: 3.551A pdb=" N GLU s 197 " --> pdb=" O ALA s 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 99 removed outlier: 4.182A pdb=" N MET T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 123 Proline residue: T 107 - end of helix removed outlier: 4.050A pdb=" N SER T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS T 111 " --> pdb=" O PRO T 107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU T 114 " --> pdb=" O SER T 110 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 157 removed outlier: 3.742A pdb=" N ASP T 146 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU T 157 " --> pdb=" O GLN T 153 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 176 removed outlier: 4.394A pdb=" N CYS T 173 " --> pdb=" O ALA T 169 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR T 174 " --> pdb=" O GLN T 170 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR T 175 " --> pdb=" O LEU T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 201 removed outlier: 3.849A pdb=" N GLY T 193 " --> pdb=" O HIS T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 205 through 215 Processing helix chain 'T' and resid 227 through 236 removed outlier: 3.820A pdb=" N LEU T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) Processing helix chain 'T' and resid 241 through 252 removed outlier: 4.693A pdb=" N ILE T 251 " --> pdb=" O ALA T 247 " (cutoff:3.500A) Proline residue: T 252 - end of helix Processing helix chain 'T' and resid 255 through 278 removed outlier: 4.010A pdb=" N LEU T 264 " --> pdb=" O ASP T 261 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP T 269 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU T 276 " --> pdb=" O GLY T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 291 Processing helix chain 'T' and resid 297 through 305 Processing helix chain 'T' and resid 333 through 347 removed outlier: 3.958A pdb=" N LYS T 337 " --> pdb=" O THR T 333 " (cutoff:3.500A) Processing helix chain 't' and resid 58 through 79 Processing helix chain 't' and resid 85 through 99 removed outlier: 3.995A pdb=" N ARG t 99 " --> pdb=" O ILE t 95 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 152 Proline residue: t 147 - end of helix Processing helix chain 't' and resid 168 through 185 Processing helix chain 'U' and resid 13 through 26 Processing helix chain 'U' and resid 72 through 83 removed outlier: 4.370A pdb=" N GLY U 80 " --> pdb=" O GLU U 76 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET U 81 " --> pdb=" O ASN U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 114 removed outlier: 3.832A pdb=" N GLU U 110 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU U 111 " --> pdb=" O ALA U 107 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG U 114 " --> pdb=" O GLU U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 178 removed outlier: 5.326A pdb=" N ASP U 178 " --> pdb=" O HIS U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 216 removed outlier: 3.629A pdb=" N VAL U 195 " --> pdb=" O ILE U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 235 removed outlier: 3.718A pdb=" N GLN U 229 " --> pdb=" O GLN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 245 through 294 removed outlier: 3.512A pdb=" N TYR U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU U 265 " --> pdb=" O TYR U 261 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU U 294 " --> pdb=" O GLY U 290 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 77 removed outlier: 3.950A pdb=" N LEU u 77 " --> pdb=" O ASP u 73 " (cutoff:3.500A) Processing helix chain 'u' and resid 85 through 101 Processing helix chain 'u' and resid 140 through 145 Processing helix chain 'u' and resid 147 through 154 Processing helix chain 'u' and resid 162 through 179 Processing helix chain 'u' and resid 210 through 213 Processing helix chain 'V' and resid 35 through 48 Processing helix chain 'V' and resid 89 through 102 removed outlier: 3.818A pdb=" N MET V 98 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR V 102 " --> pdb=" O MET V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 134 removed outlier: 3.559A pdb=" N THR V 129 " --> pdb=" O VAL V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 194 Processing helix chain 'V' and resid 211 through 221 removed outlier: 3.516A pdb=" N LYS V 215 " --> pdb=" O GLU V 211 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN V 219 " --> pdb=" O LYS V 215 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU V 220 " --> pdb=" O MET V 216 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS V 221 " --> pdb=" O LEU V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 234 through 264 removed outlier: 3.561A pdb=" N LYS V 239 " --> pdb=" O SER V 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS V 240 " --> pdb=" O GLU V 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU V 251 " --> pdb=" O GLU V 247 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS V 253 " --> pdb=" O LEU V 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN V 254 " --> pdb=" O GLU V 250 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS V 264 " --> pdb=" O GLU V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 274 removed outlier: 3.809A pdb=" N ILE V 272 " --> pdb=" O GLU V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 307 removed outlier: 3.734A pdb=" N VAL V 290 " --> pdb=" O GLU V 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL V 307 " --> pdb=" O MET V 303 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 43 removed outlier: 3.675A pdb=" N ASP W 31 " --> pdb=" O GLN W 27 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 57 No H-bonds generated for 'chain 'W' and resid 55 through 57' Processing helix chain 'W' and resid 69 through 75 Processing helix chain 'W' and resid 86 through 99 Processing helix chain 'W' and resid 121 through 134 Processing helix chain 'W' and resid 152 through 159 Processing helix chain 'W' and resid 164 through 167 No H-bonds generated for 'chain 'W' and resid 164 through 167' Processing helix chain 'W' and resid 179 through 185 removed outlier: 3.896A pdb=" N SER W 185 " --> pdb=" O ASP W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 31 Processing helix chain 'X' and resid 81 through 102 Processing helix chain 'X' and resid 108 through 122 removed outlier: 3.949A pdb=" N TYR X 122 " --> pdb=" O TYR X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 178 removed outlier: 3.955A pdb=" N LYS X 178 " --> pdb=" O THR X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 200 removed outlier: 4.274A pdb=" N LYS X 191 " --> pdb=" O ARG X 187 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU X 192 " --> pdb=" O ASP X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 220 No H-bonds generated for 'chain 'X' and resid 218 through 220' Processing helix chain 'X' and resid 229 through 242 Processing helix chain 'Y' and resid 4 through 14 Processing helix chain 'Y' and resid 18 through 26 Proline residue: Y 23 - end of helix Processing helix chain 'Y' and resid 51 through 67 Processing helix chain 'Z' and resid 119 through 131 removed outlier: 3.931A pdb=" N SER Z 127 " --> pdb=" O ALA Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 144 Processing helix chain 'Z' and resid 157 through 169 removed outlier: 3.761A pdb=" N GLY Z 164 " --> pdb=" O ARG Z 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL Z 166 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU Z 169 " --> pdb=" O GLU Z 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 182 through 197 removed outlier: 3.684A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) Proline residue: Z 193 - end of helix Processing helix chain 'Z' and resid 204 through 209 Processing helix chain 'Z' and resid 216 through 219 No H-bonds generated for 'chain 'Z' and resid 216 through 219' Processing helix chain 'Z' and resid 227 through 238 removed outlier: 3.561A pdb=" N THR Z 234 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER Z 235 " --> pdb=" O TYR Z 232 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN Z 238 " --> pdb=" O SER Z 235 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 250 No H-bonds generated for 'chain 'Z' and resid 247 through 250' Processing helix chain 'Z' and resid 252 through 255 No H-bonds generated for 'chain 'Z' and resid 252 through 255' Processing helix chain 'Z' and resid 263 through 269 removed outlier: 3.751A pdb=" N ARG Z 267 " --> pdb=" O PRO Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 276 through 284 removed outlier: 3.974A pdb=" N GLU Z 279 " --> pdb=" O GLU Z 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR Z 283 " --> pdb=" O ASP Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 300 Processing helix chain 'Z' and resid 310 through 313 No H-bonds generated for 'chain 'Z' and resid 310 through 313' Processing helix chain 'Z' and resid 319 through 322 No H-bonds generated for 'chain 'Z' and resid 319 through 322' Processing helix chain 'Z' and resid 336 through 339 No H-bonds generated for 'chain 'Z' and resid 336 through 339' Processing helix chain 'Z' and resid 344 through 355 removed outlier: 3.655A pdb=" N HIS Z 352 " --> pdb=" O ILE Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 368 through 382 removed outlier: 4.313A pdb=" N ALA Z 373 " --> pdb=" O ARG Z 369 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Z 376 " --> pdb=" O LEU Z 372 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN Z 378 " --> pdb=" O SER Z 374 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY Z 379 " --> pdb=" O SER Z 375 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 392 Processing helix chain 'Z' and resid 398 through 401 No H-bonds generated for 'chain 'Z' and resid 398 through 401' Processing helix chain 'Z' and resid 405 through 417 removed outlier: 3.611A pdb=" N LEU Z 414 " --> pdb=" O ALA Z 410 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 433 Processing helix chain 'Z' and resid 438 through 451 removed outlier: 4.024A pdb=" N ALA Z 444 " --> pdb=" O ILE Z 440 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 469 removed outlier: 3.921A pdb=" N SER Z 467 " --> pdb=" O LEU Z 463 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP Z 468 " --> pdb=" O ALA Z 464 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR Z 469 " --> pdb=" O LEU Z 465 " (cutoff:3.500A) Processing helix chain 'Z' and resid 475 through 489 Processing helix chain 'Z' and resid 495 through 507 Proline residue: Z 503 - end of helix Processing helix chain 'Z' and resid 515 through 524 removed outlier: 3.902A pdb=" N LEU Z 520 " --> pdb=" O GLY Z 516 " (cutoff:3.500A) Processing helix chain 'Z' and resid 532 through 541 removed outlier: 3.676A pdb=" N LEU Z 539 " --> pdb=" O THR Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 552 through 565 removed outlier: 3.825A pdb=" N LEU Z 558 " --> pdb=" O TYR Z 554 " (cutoff:3.500A) Proline residue: Z 559 - end of helix removed outlier: 4.059A pdb=" N ASN Z 565 " --> pdb=" O GLY Z 561 " (cutoff:3.500A) Processing helix chain 'Z' and resid 570 through 572 No H-bonds generated for 'chain 'Z' and resid 570 through 572' Processing helix chain 'Z' and resid 574 through 579 removed outlier: 3.878A pdb=" N LEU Z 577 " --> pdb=" O GLU Z 574 " (cutoff:3.500A) Processing helix chain 'Z' and resid 591 through 594 No H-bonds generated for 'chain 'Z' and resid 591 through 594' Processing helix chain 'Z' and resid 609 through 616 Processing helix chain 'Z' and resid 656 through 661 removed outlier: 4.080A pdb=" N ILE Z 660 " --> pdb=" O GLY Z 656 " (cutoff:3.500A) Processing helix chain 'Z' and resid 674 through 680 Processing helix chain 'Z' and resid 684 through 698 Proline residue: Z 691 - end of helix removed outlier: 4.035A pdb=" N ALA Z 695 " --> pdb=" O PRO Z 691 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU Z 696 " --> pdb=" O LEU Z 692 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE Z 697 " --> pdb=" O ALA Z 693 " (cutoff:3.500A) Processing helix chain 'Z' and resid 705 through 714 removed outlier: 3.518A pdb=" N THR Z 709 " --> pdb=" O ASN Z 705 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER Z 711 " --> pdb=" O LEU Z 707 " (cutoff:3.500A) Processing helix chain 'Z' and resid 719 through 733 removed outlier: 3.622A pdb=" N MET Z 729 " --> pdb=" O SER Z 725 " (cutoff:3.500A) Processing helix chain 'Z' and resid 739 through 750 removed outlier: 4.036A pdb=" N ALA Z 742 " --> pdb=" O ALA Z 739 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA Z 743 " --> pdb=" O ARG Z 740 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU Z 745 " --> pdb=" O ALA Z 742 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG Z 746 " --> pdb=" O ALA Z 743 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU Z 748 " --> pdb=" O LEU Z 745 " (cutoff:3.500A) Processing helix chain 'Z' and resid 756 through 770 Processing helix chain 'Z' and resid 790 through 795 removed outlier: 3.507A pdb=" N GLY Z 795 " --> pdb=" O VAL Z 791 " (cutoff:3.500A) Processing helix chain 'Z' and resid 797 through 805 Processing helix chain 'Z' and resid 820 through 823 removed outlier: 4.001A pdb=" N ALA Z 823 " --> pdb=" O GLY Z 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 820 through 823' Processing helix chain 'x' and resid 113 through 124 Processing helix chain 'x' and resid 126 through 133 removed outlier: 4.032A pdb=" N ALA x 131 " --> pdb=" O GLU x 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU x 132 " --> pdb=" O LEU x 128 " (cutoff:3.500A) Processing helix chain 'x' and resid 148 through 164 removed outlier: 3.515A pdb=" N ARG x 156 " --> pdb=" O THR x 152 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS x 164 " --> pdb=" O ASP x 160 " (cutoff:3.500A) Processing helix chain 'x' and resid 173 through 181 removed outlier: 3.593A pdb=" N ALA x 181 " --> pdb=" O PHE x 177 " (cutoff:3.500A) Processing helix chain 'x' and resid 199 through 213 Processing helix chain 'x' and resid 241 through 246 Processing helix chain 'x' and resid 285 through 289 Processing helix chain 'x' and resid 355 through 357 No H-bonds generated for 'chain 'x' and resid 355 through 357' Processing helix chain 'x' and resid 362 through 370 removed outlier: 3.560A pdb=" N SER x 368 " --> pdb=" O GLU x 364 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE x 369 " --> pdb=" O LYS x 365 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 464 removed outlier: 4.129A pdb=" N ARG x 464 " --> pdb=" O GLU x 460 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 34 Processing helix chain 'y' and resid 38 through 40 No H-bonds generated for 'chain 'y' and resid 38 through 40' Processing sheet with id= A, first strand: chain 'a' and resid 125 through 128 Processing sheet with id= B, first strand: chain 'a' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'a' and resid 20 through 22 removed outlier: 6.481A pdb=" N THR a 22 " --> pdb=" O ILE a 26 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE a 26 " --> pdb=" O THR a 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.264A pdb=" N THR B 38 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.518A pdb=" N MET B 138 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS B 78 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS B 71 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET B 80 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 69 " --> pdb=" O MET B 80 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 124 through 127 removed outlier: 3.671A pdb=" N LYS b 182 " --> pdb=" O SER b 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'b' and resid 119 through 121 removed outlier: 6.102A pdb=" N CYS b 43 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE b 36 " --> pdb=" O CYS b 43 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY b 45 " --> pdb=" O ILE b 34 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE b 34 " --> pdb=" O GLY b 45 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.074A pdb=" N GLU b 22 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.675A pdb=" N ASN C 213 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 71 through 77 Processing sheet with id= K, first strand: chain 'c' and resid 136 through 140 removed outlier: 5.824A pdb=" N ALA c 10 " --> pdb=" O ASP c 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'c' and resid 42 through 44 removed outlier: 4.067A pdb=" N ALA c 54 " --> pdb=" O GLU c 106 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE c 121 " --> pdb=" O THR c 133 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR c 133 " --> pdb=" O ILE c 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'c' and resid 28 through 30 removed outlier: 6.457A pdb=" N ILE c 30 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N MET c 34 " --> pdb=" O ILE c 30 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= O, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.174A pdb=" N LEU D 147 " --> pdb=" O TRP D 159 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS D 74 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS D 67 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL D 76 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE D 65 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'd' and resid 129 through 132 removed outlier: 4.722A pdb=" N VAL d 180 " --> pdb=" O LEU d 191 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'd' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'd' and resid 21 through 23 removed outlier: 6.243A pdb=" N SER d 23 " --> pdb=" O GLN d 27 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN d 27 " --> pdb=" O SER d 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= T, first strand: chain 'E' and resid 62 through 64 removed outlier: 3.761A pdb=" N ALA E 131 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU E 144 " --> pdb=" O TRP E 156 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'e' and resid 125 through 128 removed outlier: 6.676A pdb=" N HIS e 178 " --> pdb=" O ARG e 186 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG e 186 " --> pdb=" O HIS e 178 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG e 180 " --> pdb=" O TRP e 184 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TRP e 184 " --> pdb=" O ARG e 180 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'e' and resid 34 through 36 Processing sheet with id= W, first strand: chain 'e' and resid 98 through 105 Processing sheet with id= X, first strand: chain 'e' and resid 20 through 22 removed outlier: 6.525A pdb=" N ALA e 22 " --> pdb=" O ILE e 26 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE e 26 " --> pdb=" O ALA e 22 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 167 through 170 Processing sheet with id= Z, first strand: chain 'F' and resid 162 through 164 removed outlier: 6.430A pdb=" N CYS F 76 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU F 69 " --> pdb=" O CYS F 76 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET F 78 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE F 67 " --> pdb=" O MET F 78 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'f' and resid 135 through 139 removed outlier: 5.903A pdb=" N THR f 11 " --> pdb=" O ASP f 26 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'f' and resid 43 through 45 removed outlier: 4.231A pdb=" N ASN f 108 " --> pdb=" O PHE f 124 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL f 121 " --> pdb=" O ASP f 133 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'f' and resid 29 through 31 removed outlier: 6.579A pdb=" N GLU f 31 " --> pdb=" O ILE f 35 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE f 35 " --> pdb=" O GLU f 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 158 through 161 Processing sheet with id= AE, first strand: chain 'G' and resid 153 through 156 removed outlier: 4.225A pdb=" N ILE G 144 " --> pdb=" O CYS G 156 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE G 72 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS G 65 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE G 74 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 63 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'g' and resid 136 through 138 removed outlier: 3.748A pdb=" N ILE g 189 " --> pdb=" O GLU g 200 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'g' and resid 42 through 45 removed outlier: 3.519A pdb=" N THR g 49 " --> pdb=" O VAL g 45 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'g' and resid 28 through 30 removed outlier: 6.527A pdb=" N TYR g 30 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA g 34 " --> pdb=" O TYR g 30 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 97 through 99 removed outlier: 5.316A pdb=" N ASP H 143 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE H 149 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 120 through 123 removed outlier: 5.845A pdb=" N ASN H 114 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE H 101 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 339 through 342 removed outlier: 3.764A pdb=" N ARG H 339 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE H 215 " --> pdb=" O ILE H 341 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL H 212 " --> pdb=" O ILE H 315 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL H 317 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU H 214 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET H 319 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS H 270 " --> pdb=" O LYS H 316 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU H 318 " --> pdb=" O CYS H 270 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE H 272 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA H 320 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE H 274 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS H 236 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE H 273 " --> pdb=" O CYS H 236 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE H 238 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP H 275 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL H 240 " --> pdb=" O ASP H 275 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'h' and resid 165 through 169 removed outlier: 6.174A pdb=" N THR h 38 " --> pdb=" O GLN h 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN h 53 " --> pdb=" O THR h 38 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'h' and resid 160 through 162 removed outlier: 6.784A pdb=" N CYS h 78 " --> pdb=" O LYS h 71 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS h 71 " --> pdb=" O CYS h 78 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET h 80 " --> pdb=" O LEU h 69 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU h 69 " --> pdb=" O MET h 80 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 108 through 111 Processing sheet with id= AO, first strand: chain 'I' and resid 120 through 122 removed outlier: 3.531A pdb=" N ALA I 121 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 349 through 352 removed outlier: 3.651A pdb=" N ARG I 349 " --> pdb=" O GLY I 221 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 225 " --> pdb=" O ILE I 351 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL I 222 " --> pdb=" O VAL I 325 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL I 327 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU I 224 " --> pdb=" O VAL I 327 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET I 329 " --> pdb=" O LEU I 224 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER I 280 " --> pdb=" O LYS I 326 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE I 328 " --> pdb=" O SER I 280 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL I 282 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA I 330 " --> pdb=" O VAL I 282 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE I 284 " --> pdb=" O ALA I 330 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR I 246 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE I 283 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU I 248 " --> pdb=" O PHE I 283 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP I 285 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL I 250 " --> pdb=" O ASP I 285 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'i' and resid 159 through 162 removed outlier: 3.696A pdb=" N ASN i 213 " --> pdb=" O GLY i 216 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'i' and resid 71 through 77 Processing sheet with id= AS, first strand: chain 'J' and resid 94 through 97 removed outlier: 5.757A pdb=" N LYS J 88 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL J 76 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 313 through 316 removed outlier: 4.044A pdb=" N ARG J 313 " --> pdb=" O GLY J 185 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU J 187 " --> pdb=" O ARG J 313 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR J 189 " --> pdb=" O ILE J 315 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL J 186 " --> pdb=" O ILE J 289 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL J 291 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU J 188 " --> pdb=" O VAL J 291 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET J 293 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER J 244 " --> pdb=" O LYS J 290 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE J 292 " --> pdb=" O SER J 244 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE J 246 " --> pdb=" O ILE J 292 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA J 294 " --> pdb=" O ILE J 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N MET J 248 " --> pdb=" O ALA J 294 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR J 210 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE J 247 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE J 212 " --> pdb=" O PHE J 247 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'j' and resid 161 through 164 Processing sheet with id= AV, first strand: chain 'j' and resid 156 through 159 removed outlier: 4.192A pdb=" N LEU j 147 " --> pdb=" O TRP j 159 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS j 74 " --> pdb=" O LYS j 67 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS j 67 " --> pdb=" O CYS j 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL j 76 " --> pdb=" O ILE j 65 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE j 65 " --> pdb=" O VAL j 76 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 110 through 113 removed outlier: 5.539A pdb=" N GLY K 104 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE K 92 " --> pdb=" O GLY K 104 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 330 through 333 removed outlier: 8.043A pdb=" N ILE K 331 " --> pdb=" O GLY K 201 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU K 203 " --> pdb=" O ILE K 331 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE K 333 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR K 205 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL K 202 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL K 307 " --> pdb=" O VAL K 202 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET K 204 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET K 309 " --> pdb=" O MET K 204 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLY K 206 " --> pdb=" O MET K 309 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA K 260 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE K 308 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE K 262 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA K 310 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE K 264 " --> pdb=" O ALA K 310 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA K 226 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE K 263 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE K 228 " --> pdb=" O PHE K 263 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP K 265 " --> pdb=" O ILE K 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'k' and resid 158 through 161 Processing sheet with id= AZ, first strand: chain 'k' and resid 62 through 64 removed outlier: 3.817A pdb=" N ALA k 131 " --> pdb=" O THR k 147 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU k 144 " --> pdb=" O TRP k 156 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'L' and resid 78 through 81 removed outlier: 6.306A pdb=" N LYS L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL L 60 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 297 through 300 removed outlier: 3.599A pdb=" N ARG L 297 " --> pdb=" O GLY L 169 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU L 171 " --> pdb=" O ARG L 297 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET L 275 " --> pdb=" O CYS L 170 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU L 172 " --> pdb=" O MET L 275 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET L 277 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'l' and resid 38 through 40 Processing sheet with id= BD, first strand: chain 'l' and resid 76 through 79 Processing sheet with id= BE, first strand: chain 'M' and resid 91 through 93 removed outlier: 3.567A pdb=" N LYS M 125 " --> pdb=" O ASN M 92 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 350 through 354 removed outlier: 3.959A pdb=" N GLY M 227 " --> pdb=" O THR M 332 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR M 247 " --> pdb=" O ILE M 282 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE M 284 " --> pdb=" O THR M 247 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU M 249 " --> pdb=" O PHE M 284 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP M 286 " --> pdb=" O LEU M 249 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU M 251 " --> pdb=" O ASP M 286 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'm' and resid 158 through 161 Processing sheet with id= BH, first strand: chain 'm' and resid 153 through 156 removed outlier: 4.448A pdb=" N ILE m 144 " --> pdb=" O CYS m 156 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE m 72 " --> pdb=" O HIS m 65 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS m 65 " --> pdb=" O ILE m 72 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE m 74 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE m 63 " --> pdb=" O ILE m 74 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'N' and resid 744 through 746 Processing sheet with id= BJ, first strand: chain 'n' and resid 162 through 165 Processing sheet with id= BK, first strand: chain 'n' and resid 157 through 159 removed outlier: 6.564A pdb=" N MET n 75 " --> pdb=" O ASN n 68 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN n 68 " --> pdb=" O MET n 75 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL n 77 " --> pdb=" O LEU n 66 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU n 66 " --> pdb=" O VAL n 77 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'O' and resid 290 through 292 Processing sheet with id= BM, first strand: chain 'o' and resid 125 through 128 Processing sheet with id= BN, first strand: chain 'o' and resid 34 through 36 Processing sheet with id= BO, first strand: chain 'o' and resid 20 through 22 removed outlier: 6.498A pdb=" N THR o 22 " --> pdb=" O ILE o 26 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE o 26 " --> pdb=" O THR o 22 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'P' and resid 405 through 407 Processing sheet with id= BQ, first strand: chain 'p' and resid 124 through 127 removed outlier: 3.565A pdb=" N LYS p 182 " --> pdb=" O SER p 179 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'p' and resid 119 through 121 removed outlier: 6.133A pdb=" N CYS p 43 " --> pdb=" O PHE p 36 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N PHE p 36 " --> pdb=" O CYS p 43 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY p 45 " --> pdb=" O ILE p 34 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE p 34 " --> pdb=" O GLY p 45 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'p' and resid 20 through 22 removed outlier: 6.227A pdb=" N GLU p 22 " --> pdb=" O VAL p 26 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL p 26 " --> pdb=" O GLU p 22 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'Q' and resid 376 through 379 Processing sheet with id= BU, first strand: chain 'q' and resid 136 through 140 removed outlier: 5.834A pdb=" N ALA q 10 " --> pdb=" O ASP q 25 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL q 185 " --> pdb=" O LEU q 200 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'q' and resid 42 through 44 removed outlier: 4.032A pdb=" N ALA q 54 " --> pdb=" O GLU q 106 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE q 121 " --> pdb=" O THR q 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR q 133 " --> pdb=" O ILE q 121 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'q' and resid 28 through 30 removed outlier: 6.347A pdb=" N ILE q 30 " --> pdb=" O MET q 34 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N MET q 34 " --> pdb=" O ILE q 30 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'R' and resid 313 through 315 Processing sheet with id= BY, first strand: chain 'r' and resid 129 through 132 Processing sheet with id= BZ, first strand: chain 'r' and resid 35 through 37 Processing sheet with id= CA, first strand: chain 'r' and resid 21 through 23 removed outlier: 6.592A pdb=" N SER r 23 " --> pdb=" O GLN r 27 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN r 27 " --> pdb=" O SER r 23 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'S' and resid 416 through 418 Processing sheet with id= CC, first strand: chain 's' and resid 125 through 128 removed outlier: 6.695A pdb=" N HIS s 178 " --> pdb=" O ARG s 186 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG s 186 " --> pdb=" O HIS s 178 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG s 180 " --> pdb=" O TRP s 184 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP s 184 " --> pdb=" O ARG s 180 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 's' and resid 98 through 105 Processing sheet with id= CE, first strand: chain 's' and resid 20 through 22 removed outlier: 6.522A pdb=" N ALA s 22 " --> pdb=" O ILE s 26 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 's' and resid 34 through 38 removed outlier: 6.348A pdb=" N LEU s 41 " --> pdb=" O ILE s 37 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'T' and resid 281 through 283 Processing sheet with id= CH, first strand: chain 't' and resid 135 through 139 removed outlier: 5.930A pdb=" N THR t 11 " --> pdb=" O ASP t 26 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 't' and resid 130 through 133 removed outlier: 3.736A pdb=" N VAL t 121 " --> pdb=" O ASP t 133 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN t 108 " --> pdb=" O PHE t 124 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR t 50 " --> pdb=" O THR t 47 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE t 52 " --> pdb=" O LYS t 45 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS t 45 " --> pdb=" O ILE t 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS t 54 " --> pdb=" O CYS t 43 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS t 43 " --> pdb=" O CYS t 54 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 't' and resid 29 through 31 removed outlier: 6.515A pdb=" N GLU t 31 " --> pdb=" O ILE t 35 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE t 35 " --> pdb=" O GLU t 31 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'U' and resid 8 through 11 removed outlier: 6.713A pdb=" N LEU U 40 " --> pdb=" O SER U 51 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER U 53 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL U 38 " --> pdb=" O SER U 53 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA U 55 " --> pdb=" O VAL U 36 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL U 36 " --> pdb=" O ALA U 55 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLY U 41 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE U 91 " --> pdb=" O GLY U 41 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'U' and resid 58 through 60 Processing sheet with id= CM, first strand: chain 'U' and resid 121 through 124 removed outlier: 4.037A pdb=" N ALA U 137 " --> pdb=" O VAL U 158 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'u' and resid 136 through 138 removed outlier: 3.665A pdb=" N ILE u 189 " --> pdb=" O GLU u 200 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'u' and resid 42 through 45 removed outlier: 3.513A pdb=" N THR u 49 " --> pdb=" O VAL u 45 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'u' and resid 28 through 30 removed outlier: 6.650A pdb=" N TYR u 30 " --> pdb=" O ALA u 34 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA u 34 " --> pdb=" O TYR u 30 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'V' and resid 30 through 33 removed outlier: 6.829A pdb=" N LEU V 58 " --> pdb=" O ILE V 70 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL V 72 " --> pdb=" O LEU V 56 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU V 56 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA V 74 " --> pdb=" O MET V 54 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET V 54 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY V 110 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY V 59 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL V 108 " --> pdb=" O GLY V 59 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'V' and resid 142 through 145 Processing sheet with id= CS, first strand: chain 'W' and resid 136 through 142 removed outlier: 6.487A pdb=" N MET W 107 " --> pdb=" O ASN W 137 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP W 139 " --> pdb=" O MET W 107 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE W 109 " --> pdb=" O ASP W 139 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE W 141 " --> pdb=" O ILE W 109 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA W 111 " --> pdb=" O ILE W 141 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN W 48 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL W 8 " --> pdb=" O ASN W 48 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY W 50 " --> pdb=" O VAL W 8 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL W 10 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE W 52 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR W 53 " --> pdb=" O VAL W 60 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL W 60 " --> pdb=" O THR W 53 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'X' and resid 162 through 165 Processing sheet with id= CU, first strand: chain 'X' and resid 157 through 159 removed outlier: 6.762A pdb=" N MET X 75 " --> pdb=" O ASN X 68 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASN X 68 " --> pdb=" O MET X 75 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL X 77 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU X 66 " --> pdb=" O VAL X 77 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'x' and resid 265 through 269 removed outlier: 3.540A pdb=" N ARG x 318 " --> pdb=" O GLU x 249 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU x 251 " --> pdb=" O ILE x 316 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE x 316 " --> pdb=" O GLU x 251 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR x 253 " --> pdb=" O SER x 314 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER x 314 " --> pdb=" O THR x 253 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS x 255 " --> pdb=" O LYS x 312 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS x 312 " --> pdb=" O LYS x 255 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU x 295 " --> pdb=" O LYS x 312 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'x' and resid 273 through 275 removed outlier: 7.975A pdb=" N LEU x 274 " --> pdb=" O TYR x 322 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR x 324 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL x 476 " --> pdb=" O LEU x 423 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY x 480 " --> pdb=" O LEU x 419 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU x 419 " --> pdb=" O GLY x 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP x 438 " --> pdb=" O VAL x 422 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN x 426 " --> pdb=" O HIS x 434 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'x' and resid 445 through 450 removed outlier: 3.817A pdb=" N SER x 455 " --> pdb=" O LYS x 448 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'y' and resid 12 through 16 4838 hydrogen bonds defined for protein. 13620 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: 49.93 Time building geometry restraints manager: 37.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.28: 16749 1.28 - 1.44: 26574 1.44 - 1.60: 55770 1.60 - 1.76: 72 1.76 - 1.92: 774 Bond restraints: 99939 Sorted by residual: bond pdb=" N ASP L 116 " pdb=" CA ASP L 116 " ideal model delta sigma weight residual 1.457 1.253 0.203 1.41e-02 5.03e+03 2.08e+02 bond pdb=" C GLY y 75 " pdb=" N GLZ y 76 " ideal model delta sigma weight residual 1.329 1.530 -0.201 1.40e-02 5.10e+03 2.05e+02 bond pdb=" CA GLY t 53 " pdb=" C GLY t 53 " ideal model delta sigma weight residual 1.517 1.602 -0.085 7.00e-03 2.04e+04 1.47e+02 bond pdb=" C VAL o 13 " pdb=" O VAL o 13 " ideal model delta sigma weight residual 1.236 1.119 0.117 1.03e-02 9.43e+03 1.28e+02 bond pdb=" CA VAL L 115 " pdb=" CB VAL L 115 " ideal model delta sigma weight residual 1.540 1.397 0.143 1.36e-02 5.41e+03 1.10e+02 ... (remaining 99934 not shown) Histogram of bond angle deviations from ideal: 68.32 - 82.88: 2 82.88 - 97.43: 54 97.43 - 111.99: 45389 111.99 - 126.55: 89087 126.55 - 141.10: 785 Bond angle restraints: 135317 Sorted by residual: angle pdb=" CA VAL L 115 " pdb=" C VAL L 115 " pdb=" N ASP L 116 " ideal model delta sigma weight residual 116.60 68.32 48.28 1.45e+00 4.76e-01 1.11e+03 angle pdb=" C VAL L 115 " pdb=" N ASP L 116 " pdb=" CA ASP L 116 " ideal model delta sigma weight residual 121.80 76.64 45.16 2.44e+00 1.68e-01 3.43e+02 angle pdb=" O VAL L 115 " pdb=" C VAL L 115 " pdb=" N ASP L 116 " ideal model delta sigma weight residual 122.57 140.04 -17.47 1.25e+00 6.40e-01 1.95e+02 angle pdb=" O ASN O 62 " pdb=" C ASN O 62 " pdb=" N PHE O 63 " ideal model delta sigma weight residual 122.36 103.88 18.48 1.34e+00 5.57e-01 1.90e+02 angle pdb=" N ASP M 169 " pdb=" CA ASP M 169 " pdb=" C ASP M 169 " ideal model delta sigma weight residual 110.64 128.08 -17.44 1.48e+00 4.57e-01 1.39e+02 ... (remaining 135312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.75: 57618 29.75 - 59.50: 2801 59.50 - 89.26: 187 89.26 - 119.01: 18 119.01 - 148.76: 20 Dihedral angle restraints: 60644 sinusoidal: 21462 harmonic: 39182 Sorted by residual: dihedral pdb=" CA ASN R 14 " pdb=" C ASN R 14 " pdb=" N PRO R 15 " pdb=" CA PRO R 15 " ideal model delta harmonic sigma weight residual -180.00 -45.68 -134.32 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA SER K 149 " pdb=" C SER K 149 " pdb=" N SER K 150 " pdb=" CA SER K 150 " ideal model delta harmonic sigma weight residual -180.00 -47.12 -132.88 0 5.00e+00 4.00e-02 7.06e+02 dihedral pdb=" CA THR I 105 " pdb=" C THR I 105 " pdb=" N PRO I 106 " pdb=" CA PRO I 106 " ideal model delta harmonic sigma weight residual 180.00 49.92 130.08 0 5.00e+00 4.00e-02 6.77e+02 ... (remaining 60641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 12948 0.121 - 0.243: 2473 0.243 - 0.364: 265 0.364 - 0.486: 35 0.486 - 0.607: 6 Chirality restraints: 15727 Sorted by residual: chirality pdb=" CA PRO W 23 " pdb=" N PRO W 23 " pdb=" C PRO W 23 " pdb=" CB PRO W 23 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA ARG Q 33 " pdb=" N ARG Q 33 " pdb=" C ARG Q 33 " pdb=" CB ARG Q 33 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" C1' ADP J 501 " pdb=" C2' ADP J 501 " pdb=" N9 ADP J 501 " pdb=" O4' ADP J 501 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 15724 not shown) Planarity restraints: 17535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 62 " -0.096 2.00e-02 2.50e+03 1.72e-01 2.94e+02 pdb=" C ASN O 62 " 0.297 2.00e-02 2.50e+03 pdb=" O ASN O 62 " -0.116 2.00e-02 2.50e+03 pdb=" N PHE O 63 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 115 " 0.042 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C VAL L 115 " -0.225 2.00e-02 2.50e+03 pdb=" O VAL L 115 " 0.109 2.00e-02 2.50e+03 pdb=" N ASP L 116 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY y 75 " 0.062 2.00e-02 2.50e+03 1.19e-01 1.41e+02 pdb=" C GLY y 75 " -0.205 2.00e-02 2.50e+03 pdb=" O GLY y 75 " 0.083 2.00e-02 2.50e+03 pdb=" N GLZ y 76 " 0.059 2.00e-02 2.50e+03 ... (remaining 17532 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 82 1.84 - 2.60: 2717 2.60 - 3.37: 139631 3.37 - 4.13: 246580 4.13 - 4.90: 437992 Nonbonded interactions: 827002 Sorted by model distance: nonbonded pdb=" CG ASP H 133 " pdb=" NZ LYS x 344 " model vdw 1.073 3.350 nonbonded pdb=" CB ASP H 133 " pdb=" NZ LYS x 344 " model vdw 1.113 3.520 nonbonded pdb=" NE2 HIS L 323 " pdb=" CD2 PHE L 361 " model vdw 1.178 3.420 nonbonded pdb=" CD1 ILE R 229 " pdb=" CE1 TYR R 295 " model vdw 1.204 3.760 nonbonded pdb=" CD2 TYR U 79 " pdb=" CD1 ILE U 91 " model vdw 1.251 3.760 ... (remaining 826997 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 'B' and (resid 2 through 61 or (resid 62 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 245)) selection = (chain 'h' and (resid 2 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (n \ ame N or name CA or name C or name O or name CB )) or resid 60 through 245)) } ncs_group { reference = (chain 'C' and resid 1 through 231) selection = (chain 'i' and (resid 1 through 50 or (resid 51 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 161 or (resid 162 and (n \ ame N or name CA or name C or name O or name CB )) or resid 163 through 182 or ( \ resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 191 or (resid 192 and (name N or name CA or name C or name O or name CB \ )) or resid 193 or (resid 194 through 195 and (name N or name CA or name C or na \ me O or name CB )) or resid 196 through 197 or (resid 198 through 199 and (name \ N or name CA or name C or name O or name CB )) or resid 200 or (resid 201 and (n \ ame N or name CA or name C or name O or name CB )) or resid 202 through 224 or ( \ resid 225 through 226 and (name N or name CA or name C or name O or name CB )) o \ r resid 227 through 228 or (resid 229 through 231 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 251)) selection = (chain 'j' and (resid 2 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 251)) } ncs_group { reference = (chain 'E' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 or (resid 56 and (name N or na \ me CA or name C or name O or name CB )) or resid 57 through 60 or (resid 61 and \ (name N or name CA or name C or name O or name CB )) or resid 62 through 67 or ( \ resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 th \ rough 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) o \ r resid 85 through 136 or (resid 137 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 187 or (resid 188 through 189 and \ (name N or name CA or name C or name O or name CB )) or resid 190 through 210 o \ r (resid 211 through 213 and (name N or name CA or name C or name O or name CB ) \ ) or resid 214 through 223 or (resid 224 through 227 and (name N or name CA or n \ ame C or name O or name CB )) or resid 228 through 230 or (resid 231 through 244 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'k' and (resid 2 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 135 or (resid 136 throug \ h 138 and (name N or name CA or name C or name O or name CB )) or resid 139 thro \ ugh 244)) } ncs_group { reference = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 9 and (name N or name CA or name C or name CB or name CG or name OD1 \ or name OD2)) or resid 10 or (resid 11 and (name N or name CA or name C )) or r \ esid 12 through 14 or (resid 15 and (name N or name CA or name C or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 16 \ or (resid 17 and (name N or name CA or name C or name CB or name CG or name CD \ )) or resid 18 through 32 or (resid 33 and (name N or name CA or name C or name \ CB or name CG or name CD1 or name CD2)) or resid 34 through 44 or (resid 45 and \ (name N or name CA or name C )) or resid 46 through 48 or (resid 49 and (name N \ or name CA or name C or name CB )) or resid 50 or (resid 51 and (name N or name \ CA or name C or name CB or name CG or name CD or name OE1 or name OE2)) or resid \ 52 or (resid 53 and (name N or name CA or name C or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2)) or resid 54 or (resid 55 and \ (name N or name CA or name C or name CB or name OG1 or name CG2)) or resid 56 th \ rough 57 or (resid 58 and (name N or name CA or name C or name CB or name CG or \ name CD1 or name CD2)) or resid 59 through 60 or (resid 61 and (name N or name C \ A or name C or name CB or name CG or name CD )) or resid 62 through 64 or (resid \ 65 and (name N or name CA or name C or name CB or name CG or name CD or name OE \ 1 or name OE2)) or resid 66 through 73 or (resid 74 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 75 through 85 or \ (resid 86 and (name N or name CA or name C or name CB )) or resid 87 through 100 \ or (resid 101 and (name N or name CA or name C or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 102 through 110 or \ (resid 111 and (name N or name CA or name C or name CB or name OG )) or resid 11 \ 2 through 113 or (resid 114 and (name N or name CA or name C or name CB or name \ CG or name CD or name OE1 or name NE2)) or resid 115 through 118 or (resid 119 a \ nd (name N or name CA or name C or name CB or name CG or name CD1 or name CD2)) \ or (resid 120 and (name N or name CA or name C or name CB )) or resid 121 throug \ h 123 or (resid 124 and (name N or name CA or name C )) or resid 125 or (resid 1 \ 26 and (name N or name CA or name C or name CB or name CG or name CD or name OE1 \ or name OE2)) or (resid 127 and (name N or name CA or name C or name CB or name \ CG or name OD1 or name OD2)) or resid 128 through 129 or (resid 130 and (name N \ or name CA or name C or name CB or name CG or name CD )) or (resid 131 and (nam \ e N or name CA or name C )) or resid 132 through 137 or (resid 138 and (name N o \ r name CA or name C )) or resid 139 through 144 or (resid 145 and (name N or nam \ e CA or name C )) or resid 146 through 155 or (resid 156 and (name N or name CA \ or name C or name CB or name CG or name SD or name CE )) or resid 157 or (resid \ 158 and (name N or name CA or name C or name CB or name CG or name CD )) or (res \ id 159 and (name N or name CA or name C or name CB or name OG )) or (resid 160 a \ nd (name N or name CA or name C )) or resid 161 through 169 or (resid 170 and (n \ ame N or name CA or name C or name CB or name CG1 or name CG2 or name CD1)) or r \ esid 171 through 185 or (resid 186 and (name N or name CA or name C or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2)) or resid 187 or (res \ id 188 and (name N or name CA or name C or name CB or name OG )) or resid 189 or \ (resid 190 and (name N or name CA or name C or name CB or name OG1 or name CG2) \ ) or (resid 191 and (name N or name CA or name C or name CB or name CG or name C \ D1 or name CD2)) or resid 192 or (resid 193 and (name N or name CA or name C or \ name CB or name CG or name CD or name OE1 or name OE2)) or resid 194 through 206 \ or (resid 207 and (name N or name CA or name C or name CB or name CG or name CD \ or name OE1 or name OE2)) or (resid 208 through 209 and (name N or name CA or n \ ame C )) or (resid 210 and (name N or name CA or name C or name CB or name CG or \ name CD1 or name CD2)) or resid 211 through 241)) selection = (chain 'l' and (resid 8 through 207 or (resid 208 through 209 and (name N or nam \ e CA or name C )) or resid 210 through 241)) } ncs_group { reference = chain 'G' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'n' } 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' selection = (chain 's' and (resid 1 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 201)) } ncs_group { reference = chain 'f' selection = (chain 't' and (resid 1 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 213)) } ncs_group { reference = (chain 'g' and (resid 1 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 216)) selection = (chain 'u' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.970 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: 0.070 Extract box with map and model: 31.140 Check model and map are aligned: 1.160 Set scattering table: 0.690 Process input model: 229.420 Find NCS groups from input model: 7.110 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.016 0.203 99939 Z= 1.082 Angle : 1.828 48.282 135317 Z= 1.129 Chirality : 0.094 0.607 15727 Planarity : 0.009 0.183 17535 Dihedral : 16.699 148.760 35366 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 47.82 Ramachandran Plot: Outliers : 4.21 % Allowed : 11.32 % Favored : 84.47 % Rotamer: Outliers : 10.02 % Allowed : 10.23 % Favored : 79.74 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 2.64 % Twisted General : 0.25 % 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: -4.17 (0.06), residues: 13373 helix: -2.85 (0.05), residues: 5893 sheet: -1.23 (0.11), residues: 1994 loop : -3.13 (0.07), residues: 5486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.009 TRP g 209 HIS 0.026 0.005 HIS p 116 PHE 0.075 0.009 PHE a 155 TYR 0.080 0.010 TYR h 23 ARG 0.041 0.003 ARG H 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26746 Ramachandran restraints generated. 13373 Oldfield, 0 Emsley, 13373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26746 Ramachandran restraints generated. 13373 Oldfield, 0 Emsley, 13373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3694 residues out of total 11543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 952 poor density : 2742 time to evaluate : 9.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "LEU l 33 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG l 53 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP l 127 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET l 156 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU l 207 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU l 208 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS l 209 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable