Starting phenix.real_space_refine on Sun Dec 10 01:47:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/12_2023/6yam_10761_updated.pdb" } resolution = 3.6 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 1865 5.49 5 Mg 1 5.21 5 S 426 5.16 5 C 67568 2.51 5 N 21382 2.21 5 O 27286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l ARG 9": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "S PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 80": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j GLU 48": "OE1" <-> "OE2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ARG 96": "NH1" <-> "NH2" Residue "k ARG 101": "NH1" <-> "NH2" Residue "k GLU 151": "OE1" <-> "OE2" Residue "k TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 190": "NH1" <-> "NH2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k ARG 267": "NH1" <-> "NH2" Residue "k TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 306": "NH1" <-> "NH2" Residue "k GLU 320": "OE1" <-> "OE2" Residue "k ARG 325": "NH1" <-> "NH2" Residue "k GLU 335": "OE1" <-> "OE2" Residue "k GLU 340": "OE1" <-> "OE2" Residue "k GLU 341": "OE1" <-> "OE2" Residue "k GLU 359": "OE1" <-> "OE2" Residue "k ARG 390": "NH1" <-> "NH2" Residue "k ARG 395": "NH1" <-> "NH2" Residue "k ARG 502": "NH1" <-> "NH2" Residue "k ARG 531": "NH1" <-> "NH2" Residue "k PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 563": "OE1" <-> "OE2" Residue "k ARG 567": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "m ARG 183": "NH1" <-> "NH2" Residue "m ARG 212": "NH1" <-> "NH2" Residue "m ARG 218": "NH1" <-> "NH2" Residue "m ARG 271": "NH1" <-> "NH2" Residue "m ARG 329": "NH1" <-> "NH2" Residue "m ARG 362": "NH1" <-> "NH2" Residue "m ARG 402": "NH1" <-> "NH2" Residue "m ARG 434": "NH1" <-> "NH2" Residue "m ARG 462": "NH1" <-> "NH2" Residue "m GLU 475": "OE1" <-> "OE2" Residue "y ARG 7": "NH1" <-> "NH2" Residue "y ARG 158": "NH1" <-> "NH2" Residue "y ASP 176": "OD1" <-> "OD2" Residue "y GLU 248": "OE1" <-> "OE2" Residue "y ARG 321": "NH1" <-> "NH2" Residue "y ASP 345": "OD1" <-> "OD2" Residue "y ARG 353": "NH1" <-> "NH2" Residue "y ARG 354": "NH1" <-> "NH2" Residue "y PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 323": "OE1" <-> "OE2" Residue "v ARG 340": "NH1" <-> "NH2" Residue "v TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 396": "OE1" <-> "OE2" Residue "v PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 429": "OE1" <-> "OE2" Residue "v GLU 449": "OE1" <-> "OE2" Residue "v ARG 450": "NH1" <-> "NH2" Residue "v ASP 452": "OD1" <-> "OD2" Residue "v TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 484": "OE1" <-> "OE2" Residue "v GLU 491": "OE1" <-> "OE2" Residue "v TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 115": "NH1" <-> "NH2" Residue "r ARG 280": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 118536 Number of models: 1 Model: "" Number of chains: 51 Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 208} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "V" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1112 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1107 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "a" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 76} Chain: "d" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain: "n" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 37187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1743, 37187 Inner-chain residues flagged as termini: ['pdbres=" G 2 270 "', 'pdbres=" G 21765 "'] Classifications: {'RNA': 1743} Modifications used: {'5*END': 3, 'rna2p_pur': 149, 'rna2p_pyr': 121, 'rna3p': 1, 'rna3p_pur': 764, 'rna3p_pyr': 708} Link IDs: {'rna2p': 270, 'rna3p': 1472} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3214 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 394} Chain: "j" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 882 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "k" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4693 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 561} Chain: "U" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1194 Classifications: {'peptide': 145} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 130} Chain: "3" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 960 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 33} Chain: "m" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2955 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain: "y" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4971 Classifications: {'peptide': 603} Link IDs: {'CIS': 2, 'PTRANS': 23, 'TRANS': 577} Chain: "v" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4508 Classifications: {'peptide': 554} Link IDs: {'CIS': 4, 'PTRANS': 18, 'TRANS': 531} Chain: "w" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3465 Classifications: {'peptide': 419} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 403} Chain: "q" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 257} Chain: "r" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2624 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 13, 'TRANS': 307} Chain: "s" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1737 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 208} Chain: "t" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3109 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "u" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2918 Classifications: {'peptide': 365} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 354} Chain: "k" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 81 Unusual residues: {' MG': 1, 'GNP': 2, 'SF4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 82265 SG CYS k 29 115.865 104.735 82.845 1.00 0.82 S ATOM 82465 SG CYS k 55 120.689 105.533 78.494 1.00 0.73 S ATOM 82501 SG CYS k 61 120.065 101.117 82.651 1.00 0.77 S ATOM 82483 SG CYS k 58 121.153 106.325 83.707 1.00 0.73 S ATOM 82235 SG CYS k 25 116.614 96.251 83.059 1.00 0.79 S ATOM 82200 SG CYS k 21 113.388 91.168 84.230 1.00 0.76 S ATOM 82533 SG CYS k 65 118.502 93.421 84.041 1.00 0.68 S ATOM 82160 SG CYS k 16 117.289 91.128 78.145 1.00 0.73 S Residues with excluded nonbonded symmetry interactions: 413 residue: pdb=" N GLN B 52 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN B 52 " occ=0.00 residue: pdb=" N ALA B 53 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 53 " occ=0.00 residue: pdb=" N THR B 54 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 54 " occ=0.00 residue: pdb=" N ILE B 55 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 55 " occ=0.00 residue: pdb=" N ASN B 56 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 56 " occ=0.00 residue: pdb=" N ILE B 57 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 57 " occ=0.00 residue: pdb=" N GLY B 58 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 58 " occ=0.00 residue: pdb=" N THR B 59 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 59 " occ=0.00 residue: pdb=" N ILE B 60 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 60 " occ=0.00 residue: pdb=" N GLY B 61 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 61 " occ=0.00 residue: pdb=" N HIS B 62 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 62 " occ=0.00 residue: pdb=" N VAL B 63 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 63 " occ=0.00 ... (remaining 401 not shown) Time building chain proxies: 44.84, per 1000 atoms: 0.38 Number of scatterers: 118536 At special positions: 0 Unit cell: (233.2, 235.4, 338.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 426 16.00 P 1865 15.00 Mg 1 11.99 O 27286 8.00 N 21382 7.00 C 67568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.11 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 k 701 " pdb="FE3 SF4 k 701 " - pdb=" SG CYS k 61 " pdb="FE2 SF4 k 701 " - pdb=" SG CYS k 55 " pdb="FE4 SF4 k 701 " - pdb=" SG CYS k 58 " pdb="FE1 SF4 k 701 " - pdb=" SG CYS k 29 " pdb=" SF4 k 702 " pdb="FE3 SF4 k 702 " - pdb=" SG CYS k 65 " pdb="FE2 SF4 k 702 " - pdb=" SG CYS k 21 " pdb="FE1 SF4 k 702 " - pdb=" SG CYS k 25 " pdb="FE4 SF4 k 702 " - pdb=" SG CYS k 16 " Number of angles added : 24 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18460 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 343 helices and 84 sheets defined 48.3% alpha, 13.1% beta 504 base pairs and 888 stacking pairs defined. Time for finding SS restraints: 66.42 Creating SS restraints... Processing helix chain 'l' and resid 1 through 25 removed outlier: 3.573A pdb=" N MET l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.883A pdb=" N VAL C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 39 removed outlier: 3.578A pdb=" N GLU C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 39' Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.775A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 removed outlier: 4.428A pdb=" N ARG C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.670A pdb=" N SER C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 186 removed outlier: 4.424A pdb=" N GLY C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 removed outlier: 3.516A pdb=" N LYS D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 29' Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.539A pdb=" N GLY D 61 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.716A pdb=" N LEU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 4.084A pdb=" N MET D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS D 115 " --> pdb=" O CYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 3.546A pdb=" N VAL D 161 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.577A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.571A pdb=" N ILE D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER D 203 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.784A pdb=" N GLU D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.522A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 4.171A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 83 removed outlier: 4.971A pdb=" N ILE E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.840A pdb=" N ALA E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.633A pdb=" N LYS E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 235 removed outlier: 3.800A pdb=" N PHE E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.997A pdb=" N TRP E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS E 242 " --> pdb=" O PRO E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 237 through 242' Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.909A pdb=" N THR E 255 " --> pdb=" O TYR E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.792A pdb=" N VAL E 259 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS E 260 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR E 261 " --> pdb=" O LEU E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'F' and resid 6 through 29 removed outlier: 3.764A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.921A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 removed outlier: 3.556A pdb=" N PHE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.950A pdb=" N CYS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 98' Processing helix chain 'F' and resid 99 through 112 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.697A pdb=" N ALA F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.221A pdb=" N TYR F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 50 removed outlier: 3.676A pdb=" N PHE G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.721A pdb=" N VAL G 61 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 removed outlier: 4.160A pdb=" N LYS G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 259 removed outlier: 3.529A pdb=" N ARG G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 removed outlier: 4.341A pdb=" N GLN H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 37' Processing helix chain 'H' and resid 59 through 66 removed outlier: 4.068A pdb=" N LYS H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA H 64 " --> pdb=" O ARG H 60 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 66' Processing helix chain 'H' and resid 67 through 77 removed outlier: 3.974A pdb=" N MET H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 104 removed outlier: 3.822A pdb=" N ILE H 92 " --> pdb=" O MET H 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.940A pdb=" N VAL H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 165 removed outlier: 3.586A pdb=" N LEU H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS H 155 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.984A pdb=" N GLY H 183 " --> pdb=" O ASN H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 204 removed outlier: 3.848A pdb=" N LYS H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 removed outlier: 3.620A pdb=" N LEU I 24 " --> pdb=" O ASP I 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 43 removed outlier: 4.355A pdb=" N GLY I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU I 43 " --> pdb=" O ASP I 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 38 through 43' Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.753A pdb=" N ILE I 141 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 237 removed outlier: 3.744A pdb=" N LEU I 185 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU I 237 " --> pdb=" O ARG I 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 34 removed outlier: 4.153A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 5.386A pdb=" N LEU J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 41' Processing helix chain 'J' and resid 65 through 76 removed outlier: 6.535A pdb=" N LEU J 69 " --> pdb=" O PRO J 65 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 72 " --> pdb=" O GLN J 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J 74 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 88 removed outlier: 3.664A pdb=" N SER J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 122 removed outlier: 6.596A pdb=" N LEU J 122 " --> pdb=" O ARG J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 135 removed outlier: 3.866A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL J 134 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 168 removed outlier: 4.162A pdb=" N VAL J 166 " --> pdb=" O GLN J 162 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS J 168 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 removed outlier: 4.336A pdb=" N SER J 174 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 176 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 removed outlier: 5.670A pdb=" N VAL J 9 " --> pdb=" O ALA J 6 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS J 10 " --> pdb=" O LYS J 7 " (cutoff:3.500A) Proline residue: J 11 - end of helix No H-bonds generated for 'chain 'J' and resid 6 through 11' Processing helix chain 'K' and resid 87 through 94 removed outlier: 4.910A pdb=" N VAL K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG K 92 " --> pdb=" O ASN K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.976A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 132 removed outlier: 4.783A pdb=" N LEU K 129 " --> pdb=" O LYS K 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR K 130 " --> pdb=" O GLY K 126 " (cutoff:3.500A) Proline residue: K 131 - end of helix No H-bonds generated for 'chain 'K' and resid 125 through 132' Processing helix chain 'K' and resid 133 through 138 removed outlier: 4.119A pdb=" N LEU K 137 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 153 removed outlier: 4.654A pdb=" N LYS K 148 " --> pdb=" O LYS K 144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR K 149 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 169 removed outlier: 4.265A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 removed outlier: 3.547A pdb=" N GLU K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 36 removed outlier: 3.608A pdb=" N ASP L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 removed outlier: 3.951A pdb=" N VAL L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU L 60 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR L 62 " --> pdb=" O ARG L 58 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 85 removed outlier: 3.554A pdb=" N ARG L 79 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 4.286A pdb=" N ILE L 97 " --> pdb=" O LYS L 93 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS L 101 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 110 removed outlier: 3.908A pdb=" N LEU L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG L 109 " --> pdb=" O PHE L 105 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 117 Processing helix chain 'L' and resid 122 through 133 removed outlier: 3.539A pdb=" N ALA L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG L 133 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 removed outlier: 3.832A pdb=" N GLN L 154 " --> pdb=" O ARG L 150 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 150 through 155' Processing helix chain 'L' and resid 171 through 183 removed outlier: 3.643A pdb=" N LYS L 176 " --> pdb=" O ARG L 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.905A pdb=" N ARG M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE M 9 " --> pdb=" O LYS M 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 16 " --> pdb=" O TYR M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.176A pdb=" N LYS M 47 " --> pdb=" O LEU M 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 84 Processing helix chain 'N' and resid 47 through 53 removed outlier: 3.924A pdb=" N ILE N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 26 removed outlier: 3.731A pdb=" N LEU O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS O 23 " --> pdb=" O GLN O 19 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 45 removed outlier: 4.415A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 4.839A pdb=" N VAL O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 90 removed outlier: 4.410A pdb=" N LEU O 85 " --> pdb=" O ASP O 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY O 90 " --> pdb=" O GLY O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 132 removed outlier: 4.792A pdb=" N VAL O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE O 128 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS O 131 " --> pdb=" O TYR O 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 44 removed outlier: 3.580A pdb=" N GLU P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY P 44 " --> pdb=" O LEU P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 57 removed outlier: 4.164A pdb=" N SER P 57 " --> pdb=" O ILE P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 67 removed outlier: 4.197A pdb=" N VAL P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR P 67 " --> pdb=" O VAL P 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 62 through 67' Processing helix chain 'P' and resid 70 through 79 removed outlier: 3.545A pdb=" N ILE P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 removed outlier: 3.556A pdb=" N VAL P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG P 106 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 133 removed outlier: 3.616A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 117 " --> pdb=" O PHE P 113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS P 132 " --> pdb=" O TYR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 151 removed outlier: 3.654A pdb=" N ALA P 151 " --> pdb=" O SER P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Proline residue: P 23 - end of helix No H-bonds generated for 'chain 'P' and resid 20 through 25' Processing helix chain 'Q' and resid 57 through 62 removed outlier: 3.584A pdb=" N LYS Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 89 removed outlier: 3.679A pdb=" N ASP Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 123 removed outlier: 4.107A pdb=" N SER Q 114 " --> pdb=" O PRO Q 110 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY Q 123 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 53 removed outlier: 6.820A pdb=" N GLN S 48 " --> pdb=" O PRO S 44 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR S 49 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU S 51 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU S 52 " --> pdb=" O GLN S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 59 Processing helix chain 'S' and resid 60 through 65 removed outlier: 4.267A pdb=" N ALA S 64 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 60 through 65' Processing helix chain 'S' and resid 76 through 99 removed outlier: 3.558A pdb=" N GLN S 80 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR S 82 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 116 removed outlier: 4.118A pdb=" N LYS S 105 " --> pdb=" O ASP S 101 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR S 115 " --> pdb=" O ILE S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 20 removed outlier: 3.531A pdb=" N LYS T 10 " --> pdb=" O THR T 6 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 39 Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.903A pdb=" N ARG T 47 " --> pdb=" O SER T 43 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY T 52 " --> pdb=" O ASN T 48 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG T 63 " --> pdb=" O LYS T 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 84 removed outlier: 3.636A pdb=" N GLU T 75 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR T 84 " --> pdb=" O ARG T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 110 removed outlier: 4.007A pdb=" N LYS T 103 " --> pdb=" O ASP T 99 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU T 104 " --> pdb=" O PRO T 100 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET T 105 " --> pdb=" O ASP T 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 10 removed outlier: 4.649A pdb=" N VAL V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASN V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 5 through 10' Processing helix chain 'V' and resid 11 through 26 removed outlier: 3.992A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER V 25 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY V 26 " --> pdb=" O LEU V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 67 removed outlier: 3.612A pdb=" N ALA V 58 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU V 64 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 80 removed outlier: 3.625A pdb=" N THR V 76 " --> pdb=" O VAL V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 111 removed outlier: 5.441A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 143 removed outlier: 3.750A pdb=" N GLY V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA V 139 " --> pdb=" O ALA V 135 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS V 143 " --> pdb=" O ALA V 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 47 removed outlier: 3.848A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU W 39 " --> pdb=" O VAL W 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS W 46 " --> pdb=" O GLY W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 105 removed outlier: 3.754A pdb=" N VAL W 98 " --> pdb=" O PRO W 94 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER W 103 " --> pdb=" O LYS W 99 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE W 104 " --> pdb=" O GLN W 100 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER W 105 " --> pdb=" O ILE W 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 63 Processing helix chain 'X' and resid 64 through 77 removed outlier: 3.657A pdb=" N HIS X 76 " --> pdb=" O LEU X 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY X 77 " --> pdb=" O ALA X 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 21 removed outlier: 3.832A pdb=" N ASP Y 9 " --> pdb=" O ASN Y 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS Y 12 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 45 removed outlier: 3.555A pdb=" N VAL Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY Y 45 " --> pdb=" O MET Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 94 removed outlier: 6.332A pdb=" N LEU Y 86 " --> pdb=" O GLN Y 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS Y 88 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 120 removed outlier: 3.521A pdb=" N ALA Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 24 removed outlier: 3.875A pdb=" N HIS Z 16 " --> pdb=" O LYS Z 12 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Z 18 " --> pdb=" O ARG Z 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP Z 19 " --> pdb=" O SER Z 15 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS Z 23 " --> pdb=" O ASP Z 19 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP Z 24 " --> pdb=" O GLN Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 3.521A pdb=" N LYS Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU Z 32 " --> pdb=" O LYS Z 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 33 " --> pdb=" O LYS Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 39 Processing helix chain 'Z' and resid 89 through 95 removed outlier: 4.208A pdb=" N PHE Z 93 " --> pdb=" O GLY Z 89 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Z 94 " --> pdb=" O CYS Z 90 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU Z 95 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 89 through 95' Processing helix chain 'Z' and resid 129 through 136 Processing helix chain 'a' and resid 36 through 49 removed outlier: 3.760A pdb=" N ILE a 40 " --> pdb=" O PRO a 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 56 removed outlier: 4.366A pdb=" N ILE a 55 " --> pdb=" O THR a 51 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE a 56 " --> pdb=" O PRO a 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 51 through 56' Processing helix chain 'a' and resid 78 through 86 removed outlier: 3.846A pdb=" N ALA a 82 " --> pdb=" O SER a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 95 removed outlier: 3.663A pdb=" N LEU a 91 " --> pdb=" O PRO a 87 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS a 94 " --> pdb=" O ARG a 90 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 118 removed outlier: 3.937A pdb=" N ARG a 110 " --> pdb=" O GLN a 106 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL a 117 " --> pdb=" O ARG a 113 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG a 118 " --> pdb=" O MET a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 127 Processing helix chain 'b' and resid 46 through 57 removed outlier: 3.896A pdb=" N VAL b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG b 51 " --> pdb=" O ALA b 47 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 82 removed outlier: 3.618A pdb=" N ILE b 79 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER b 81 " --> pdb=" O CYS b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 93 removed outlier: 5.384A pdb=" N LYS b 93 " --> pdb=" O ARG b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 17 removed outlier: 4.900A pdb=" N LYS c 16 " --> pdb=" O PRO c 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 12 through 17' Processing helix chain 'e' and resid 15 through 20 removed outlier: 4.264A pdb=" N ARG e 19 " --> pdb=" O GLY e 15 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER e 20 " --> pdb=" O GLN e 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 15 through 20' Processing helix chain 'e' and resid 40 through 48 removed outlier: 3.954A pdb=" N GLN e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 65 removed outlier: 3.599A pdb=" N CYS n 59 " --> pdb=" O TYR n 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS n 60 " --> pdb=" O ASP n 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL n 62 " --> pdb=" O LEU n 58 " (cutoff:3.500A) Proline residue: n 63 - end of helix Processing helix chain 'n' and resid 69 through 77 removed outlier: 3.842A pdb=" N GLU n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 95 removed outlier: 6.552A pdb=" N ALA n 84 " --> pdb=" O ARG n 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER n 93 " --> pdb=" O GLN n 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS n 94 " --> pdb=" O GLU n 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 90 removed outlier: 3.776A pdb=" N THR i 90 " --> pdb=" O VAL i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 116 removed outlier: 4.103A pdb=" N ARG i 108 " --> pdb=" O GLY i 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG i 115 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 5.826A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 63' Processing helix chain 'A' and resid 91 through 117 removed outlier: 3.703A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 4.571A pdb=" N GLU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.888A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 6.060A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.840A pdb=" N VAL A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.676A pdb=" N LYS A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 7.104A pdb=" N GLY A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 removed outlier: 4.790A pdb=" N VAL B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 166 removed outlier: 4.231A pdb=" N VAL B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.951A pdb=" N SER B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 removed outlier: 4.269A pdb=" N GLN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.691A pdb=" N GLU B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.407A pdb=" N CYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 107 Processing helix chain 'j' and resid 10 through 16 removed outlier: 5.938A pdb=" N ARG j 13 " --> pdb=" O LYS j 10 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG j 14 " --> pdb=" O ASN j 11 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY j 15 " --> pdb=" O ARG j 12 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS j 16 " --> pdb=" O ARG j 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 10 through 16' Processing helix chain 'k' and resid 17 through 22 removed outlier: 3.713A pdb=" N CYS k 21 " --> pdb=" O LYS k 17 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG k 22 " --> pdb=" O PRO k 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 17 through 22' Processing helix chain 'k' and resid 23 through 29 removed outlier: 3.717A pdb=" N CYS k 29 " --> pdb=" O CYS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 35 removed outlier: 3.833A pdb=" N GLY k 35 " --> pdb=" O VAL k 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 65 removed outlier: 3.518A pdb=" N LYS k 64 " --> pdb=" O ILE k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 115 through 125 removed outlier: 3.551A pdb=" N GLY k 125 " --> pdb=" O LYS k 121 " (cutoff:3.500A) Processing helix chain 'k' and resid 139 through 148 removed outlier: 6.187A pdb=" N ILE k 143 " --> pdb=" O ASP k 139 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU k 144 " --> pdb=" O TRP k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 151 through 162 removed outlier: 3.703A pdb=" N TYR k 155 " --> pdb=" O GLU k 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP k 162 " --> pdb=" O LYS k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 181 Proline residue: k 177 - end of helix removed outlier: 5.919A pdb=" N ALA k 180 " --> pdb=" O ILE k 176 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LYS k 181 " --> pdb=" O PRO k 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 173 through 181' Processing helix chain 'k' and resid 184 through 192 removed outlier: 6.076A pdb=" N LEU k 188 " --> pdb=" O VAL k 184 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP k 192 " --> pdb=" O LEU k 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 194 through 205 removed outlier: 3.784A pdb=" N ALA k 198 " --> pdb=" O THR k 194 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP k 205 " --> pdb=" O CYS k 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 213 through 218 removed outlier: 4.191A pdb=" N LEU k 217 " --> pdb=" O ASN k 213 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER k 218 " --> pdb=" O VAL k 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 213 through 218' Processing helix chain 'k' and resid 219 through 233 Processing helix chain 'k' and resid 248 through 263 removed outlier: 3.604A pdb=" N LEU k 253 " --> pdb=" O VAL k 249 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU k 262 " --> pdb=" O THR k 258 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE k 263 " --> pdb=" O ILE k 259 " (cutoff:3.500A) Processing helix chain 'k' and resid 278 through 283 Processing helix chain 'k' and resid 304 through 314 removed outlier: 3.901A pdb=" N ASN k 310 " --> pdb=" O ARG k 306 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE k 311 " --> pdb=" O GLU k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 384 through 394 removed outlier: 4.279A pdb=" N PHE k 388 " --> pdb=" O GLY k 384 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE k 389 " --> pdb=" O LYS k 385 " (cutoff:3.500A) Processing helix chain 'k' and resid 423 through 432 removed outlier: 3.761A pdb=" N LEU k 427 " --> pdb=" O SER k 423 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS k 429 " --> pdb=" O ARG k 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU k 430 " --> pdb=" O GLN k 426 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS k 431 " --> pdb=" O LEU k 427 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE k 432 " --> pdb=" O LEU k 428 " (cutoff:3.500A) Processing helix chain 'k' and resid 439 through 444 removed outlier: 4.277A pdb=" N THR k 443 " --> pdb=" O PRO k 439 " (cutoff:3.500A) Processing helix chain 'k' and resid 450 through 456 removed outlier: 5.043A pdb=" N ILE k 454 " --> pdb=" O GLN k 450 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP k 456 " --> pdb=" O GLU k 452 " (cutoff:3.500A) Processing helix chain 'k' and resid 463 through 478 removed outlier: 4.037A pdb=" N CYS k 475 " --> pdb=" O ALA k 471 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU k 476 " --> pdb=" O LEU k 472 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY k 477 " --> pdb=" O ALA k 473 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS k 478 " --> pdb=" O LEU k 474 " (cutoff:3.500A) Processing helix chain 'k' and resid 494 through 512 removed outlier: 4.103A pdb=" N MET k 499 " --> pdb=" O GLU k 495 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA k 511 " --> pdb=" O PHE k 507 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS k 512 " --> pdb=" O ILE k 508 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 529 removed outlier: 4.565A pdb=" N LEU k 528 " --> pdb=" O MET k 524 " (cutoff:3.500A) Processing helix chain 'k' and resid 551 through 563 removed outlier: 3.634A pdb=" N GLN k 561 " --> pdb=" O LYS k 557 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU k 562 " --> pdb=" O PHE k 558 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU k 563 " --> pdb=" O LEU k 559 " (cutoff:3.500A) Processing helix chain 'k' and resid 582 through 592 removed outlier: 4.544A pdb=" N VAL k 586 " --> pdb=" O SER k 582 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU k 587 " --> pdb=" O ILE k 583 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS k 589 " --> pdb=" O ASP k 585 " (cutoff:3.500A) Processing helix chain 'k' and resid 206 through 211 removed outlier: 5.019A pdb=" N LEU k 209 " --> pdb=" O LEU k 206 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS k 210 " --> pdb=" O THR k 207 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU k 211 " --> pdb=" O HIS k 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 206 through 211' Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.506A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 49 removed outlier: 3.995A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG U 46 " --> pdb=" O HIS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 74 removed outlier: 3.647A pdb=" N ARG U 66 " --> pdb=" O ASP U 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Proline residue: U 74 - end of helix Processing helix chain 'U' and resid 100 through 118 removed outlier: 3.865A pdb=" N ASP U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG U 118 " --> pdb=" O LEU U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 128 removed outlier: 3.769A pdb=" N LEU U 123 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 29 removed outlier: 3.617A pdb=" N LEU R 25 " --> pdb=" O ASP R 21 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 36 removed outlier: 3.808A pdb=" N GLN R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 48 removed outlier: 4.253A pdb=" N ARG R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 67 removed outlier: 5.523A pdb=" N LEU R 56 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 121 removed outlier: 4.819A pdb=" N PHE R 119 " --> pdb=" O TYR R 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE R 121 " --> pdb=" O GLY R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 115 through 121' Processing helix chain 'm' and resid 175 through 183 removed outlier: 4.276A pdb=" N LYS m 181 " --> pdb=" O PRO m 177 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET m 182 " --> pdb=" O GLN m 178 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG m 183 " --> pdb=" O LEU m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 203 through 209 removed outlier: 4.857A pdb=" N ASP m 207 " --> pdb=" O ASP m 203 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG m 208 " --> pdb=" O LYS m 204 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE m 209 " --> pdb=" O ALA m 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 203 through 209' Processing helix chain 'm' and resid 232 through 242 removed outlier: 3.568A pdb=" N ALA m 239 " --> pdb=" O ILE m 235 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS m 240 " --> pdb=" O ARG m 236 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR m 241 " --> pdb=" O LYS m 237 " (cutoff:3.500A) Processing helix chain 'm' and resid 248 through 258 removed outlier: 3.647A pdb=" N LEU m 255 " --> pdb=" O ILE m 251 " (cutoff:3.500A) Processing helix chain 'm' and resid 308 through 329 removed outlier: 4.271A pdb=" N HIS m 321 " --> pdb=" O THR m 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN m 322 " --> pdb=" O TYR m 318 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER m 324 " --> pdb=" O ASN m 320 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN m 325 " --> pdb=" O HIS m 321 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN m 326 " --> pdb=" O ASN m 322 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU m 328 " --> pdb=" O SER m 324 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG m 329 " --> pdb=" O GLN m 325 " (cutoff:3.500A) Processing helix chain 'm' and resid 400 through 405 removed outlier: 4.725A pdb=" N CYS m 404 " --> pdb=" O ASP m 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN m 405 " --> pdb=" O SER m 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 400 through 405' Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 416 through 428 removed outlier: 3.798A pdb=" N ILE m 421 " --> pdb=" O ARG m 417 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU m 424 " --> pdb=" O VAL m 420 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS m 426 " --> pdb=" O ALA m 422 " (cutoff:3.500A) Processing helix chain 'm' and resid 429 through 443 Processing helix chain 'm' and resid 472 through 481 Processing helix chain 'm' and resid 483 through 499 removed outlier: 4.509A pdb=" N ALA m 487 " --> pdb=" O SER m 483 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY m 489 " --> pdb=" O GLU m 485 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE m 490 " --> pdb=" O ASN m 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU m 491 " --> pdb=" O ALA m 487 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE m 497 " --> pdb=" O CYS m 493 " (cutoff:3.500A) Processing helix chain 'y' and resid 8 through 22 removed outlier: 4.676A pdb=" N LEU y 12 " --> pdb=" O PRO y 8 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS y 13 " --> pdb=" O GLU y 9 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 37 removed outlier: 3.899A pdb=" N ALA y 27 " --> pdb=" O LYS y 23 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU y 28 " --> pdb=" O LYS y 24 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL y 34 " --> pdb=" O VAL y 30 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER y 37 " --> pdb=" O ASP y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 46 through 62 Processing helix chain 'y' and resid 63 through 79 removed outlier: 3.623A pdb=" N GLU y 69 " --> pdb=" O HIS y 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN y 76 " --> pdb=" O TYR y 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 82 through 118 removed outlier: 4.832A pdb=" N LEU y 86 " --> pdb=" O ASN y 82 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL y 112 " --> pdb=" O SER y 108 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU y 113 " --> pdb=" O GLN y 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP y 114 " --> pdb=" O GLN y 110 " (cutoff:3.500A) Processing helix chain 'y' and resid 124 through 132 removed outlier: 5.718A pdb=" N LEU y 128 " --> pdb=" O PRO y 124 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU y 129 " --> pdb=" O GLU y 125 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER y 130 " --> pdb=" O SER y 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA y 131 " --> pdb=" O VAL y 127 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL y 132 " --> pdb=" O LEU y 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 124 through 132' Processing helix chain 'y' and resid 136 through 146 removed outlier: 4.630A pdb=" N LEU y 144 " --> pdb=" O ARG y 140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU y 145 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 165 removed outlier: 4.218A pdb=" N LEU y 161 " --> pdb=" O TYR y 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP y 162 " --> pdb=" O ARG y 158 " (cutoff:3.500A) Processing helix chain 'y' and resid 172 through 188 removed outlier: 5.429A pdb=" N ASP y 176 " --> pdb=" O ARG y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 210 removed outlier: 4.278A pdb=" N PHE y 194 " --> pdb=" O ARG y 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG y 195 " --> pdb=" O LYS y 191 " (cutoff:3.500A) Processing helix chain 'y' and resid 221 through 244 removed outlier: 3.661A pdb=" N SER y 225 " --> pdb=" O ASN y 221 " (cutoff:3.500A) Processing helix chain 'y' and resid 245 through 264 removed outlier: 3.918A pdb=" N ALA y 249 " --> pdb=" O LEU y 245 " (cutoff:3.500A) Processing helix chain 'y' and resid 270 through 284 removed outlier: 6.223A pdb=" N ASN y 274 " --> pdb=" O GLN y 270 " (cutoff:3.500A) Processing helix chain 'y' and resid 288 through 310 Processing helix chain 'y' and resid 314 through 331 removed outlier: 3.713A pdb=" N MET y 318 " --> pdb=" O GLU y 314 " (cutoff:3.500A) Proline residue: y 330 - end of helix Processing helix chain 'y' and resid 337 through 343 Processing helix chain 'y' and resid 346 through 360 removed outlier: 6.113A pdb=" N GLU y 350 " --> pdb=" O GLY y 346 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS y 351 " --> pdb=" O ILE y 347 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN y 352 " --> pdb=" O ILE y 348 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 376 removed outlier: 3.614A pdb=" N ILE y 371 " --> pdb=" O ARG y 367 " (cutoff:3.500A) Processing helix chain 'y' and resid 378 through 383 removed outlier: 3.714A pdb=" N TYR y 382 " --> pdb=" O ASN y 378 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL y 383 " --> pdb=" O VAL y 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 378 through 383' Processing helix chain 'y' and resid 384 through 395 removed outlier: 4.751A pdb=" N ASP y 389 " --> pdb=" O PRO y 385 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU y 390 " --> pdb=" O GLU y 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR y 391 " --> pdb=" O VAL y 387 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN y 392 " --> pdb=" O LYS y 388 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP y 393 " --> pdb=" O ASP y 389 " (cutoff:3.500A) Processing helix chain 'y' and resid 402 through 416 removed outlier: 3.707A pdb=" N THR y 408 " --> pdb=" O CYS y 404 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS y 409 " --> pdb=" O GLU y 405 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL y 410 " --> pdb=" O ARG y 406 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU y 416 " --> pdb=" O ASN y 412 " (cutoff:3.500A) Processing helix chain 'y' and resid 422 through 447 removed outlier: 3.752A pdb=" N GLN y 426 " --> pdb=" O PRO y 422 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR y 427 " --> pdb=" O GLU y 423 " (cutoff:3.500A) Proline residue: y 429 - end of helix removed outlier: 3.515A pdb=" N GLN y 441 " --> pdb=" O LEU y 437 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN y 442 " --> pdb=" O ARG y 438 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL y 443 " --> pdb=" O LEU y 439 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA y 444 " --> pdb=" O LEU y 440 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN y 445 " --> pdb=" O GLN y 441 " (cutoff:3.500A) Processing helix chain 'y' and resid 451 through 460 removed outlier: 3.753A pdb=" N SER y 457 " --> pdb=" O SER y 453 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL y 459 " --> pdb=" O LEU y 455 " (cutoff:3.500A) Proline residue: y 460 - end of helix Processing helix chain 'y' and resid 463 through 478 removed outlier: 3.569A pdb=" N LEU y 467 " --> pdb=" O ASP y 463 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG y 469 " --> pdb=" O PHE y 465 " (cutoff:3.500A) Processing helix chain 'y' and resid 500 through 505 removed outlier: 4.421A pdb=" N ASP y 504 " --> pdb=" O ALA y 500 " (cutoff:3.500A) Processing helix chain 'y' and resid 522 through 539 removed outlier: 4.116A pdb=" N LYS y 532 " --> pdb=" O SER y 528 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA y 533 " --> pdb=" O VAL y 529 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU y 535 " --> pdb=" O ALA y 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL y 536 " --> pdb=" O LYS y 532 " (cutoff:3.500A) Proline residue: y 539 - end of helix Processing helix chain 'y' and resid 540 through 569 removed outlier: 5.264A pdb=" N GLN y 544 " --> pdb=" O ALA y 540 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU y 545 " --> pdb=" O HIS y 541 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS y 546 " --> pdb=" O ILE y 542 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS y 563 " --> pdb=" O LYS y 559 " (cutoff:3.500A) Processing helix chain 'y' and resid 570 through 605 removed outlier: 3.690A pdb=" N ARG y 578 " --> pdb=" O THR y 574 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG y 581 " --> pdb=" O GLU y 577 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU y 583 " --> pdb=" O LYS y 579 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER y 584 " --> pdb=" O GLU y 580 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU y 594 " --> pdb=" O GLU y 590 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU y 595 " --> pdb=" O LYS y 591 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU y 600 " --> pdb=" O GLN y 596 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU y 601 " --> pdb=" O ARG y 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS y 603 " --> pdb=" O ALA y 599 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG y 605 " --> pdb=" O LEU y 601 " (cutoff:3.500A) Processing helix chain 'v' and resid 327 through 340 removed outlier: 4.725A pdb=" N ALA v 339 " --> pdb=" O GLU v 335 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ARG v 340 " --> pdb=" O ILE v 336 " (cutoff:3.500A) Processing helix chain 'v' and resid 346 through 361 removed outlier: 5.995A pdb=" N GLN v 350 " --> pdb=" O ASP v 346 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE v 351 " --> pdb=" O ARG v 347 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU v 353 " --> pdb=" O ALA v 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL v 358 " --> pdb=" O LEU v 354 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE v 360 " --> pdb=" O LEU v 356 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA v 361 " --> pdb=" O LEU v 357 " (cutoff:3.500A) Processing helix chain 'v' and resid 365 through 385 removed outlier: 4.651A pdb=" N GLY v 369 " --> pdb=" O ASN v 365 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL v 370 " --> pdb=" O LEU v 366 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE v 371 " --> pdb=" O GLY v 367 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL v 372 " --> pdb=" O GLU v 368 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS v 373 " --> pdb=" O GLY v 369 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE v 374 " --> pdb=" O VAL v 370 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR v 385 " --> pdb=" O SER v 381 " (cutoff:3.500A) Processing helix chain 'v' and resid 394 through 415 removed outlier: 5.932A pdb=" N LEU v 412 " --> pdb=" O LEU v 408 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN v 415 " --> pdb=" O ILE v 411 " (cutoff:3.500A) Processing helix chain 'v' and resid 430 through 435 removed outlier: 5.320A pdb=" N VAL v 434 " --> pdb=" O ASN v 430 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP v 435 " --> pdb=" O LEU v 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 430 through 435' Processing helix chain 'v' and resid 436 through 462 removed outlier: 4.053A pdb=" N VAL v 440 " --> pdb=" O GLN v 436 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE v 444 " --> pdb=" O VAL v 440 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU v 445 " --> pdb=" O ARG v 441 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR v 446 " --> pdb=" O GLY v 442 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU v 447 " --> pdb=" O CYS v 443 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN v 460 " --> pdb=" O THR v 456 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN v 461 " --> pdb=" O LYS v 457 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR v 462 " --> pdb=" O ILE v 458 " (cutoff:3.500A) Processing helix chain 'v' and resid 468 through 490 removed outlier: 4.450A pdb=" N HIS v 472 " --> pdb=" O GLU v 468 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN v 487 " --> pdb=" O ILE v 483 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG v 488 " --> pdb=" O GLU v 484 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR v 489 " --> pdb=" O ARG v 485 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU v 490 " --> pdb=" O VAL v 486 " (cutoff:3.500A) Processing helix chain 'v' and resid 499 through 511 removed outlier: 3.719A pdb=" N TYR v 503 " --> pdb=" O ILE v 499 " (cutoff:3.500A) Processing helix chain 'v' and resid 514 through 523 removed outlier: 5.955A pdb=" N ARG v 521 " --> pdb=" O LYS v 517 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN v 522 " --> pdb=" O ALA v 518 " (cutoff:3.500A) Processing helix chain 'v' and resid 532 through 545 removed outlier: 3.783A pdb=" N GLN v 536 " --> pdb=" O SER v 532 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP v 543 " --> pdb=" O ASN v 539 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA v 545 " --> pdb=" O GLY v 541 " (cutoff:3.500A) Processing helix chain 'v' and resid 546 through 560 removed outlier: 3.983A pdb=" N ARG v 550 " --> pdb=" O VAL v 546 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR v 554 " --> pdb=" O ARG v 550 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE v 555 " --> pdb=" O LEU v 551 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS v 558 " --> pdb=" O TYR v 554 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP v 559 " --> pdb=" O ILE v 555 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG v 560 " --> pdb=" O TYR v 556 " (cutoff:3.500A) Processing helix chain 'v' and resid 561 through 579 removed outlier: 4.139A pdb=" N CYS v 567 " --> pdb=" O ARG v 563 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU v 570 " --> pdb=" O THR v 566 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS v 571 " --> pdb=" O CYS v 567 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR v 574 " --> pdb=" O LEU v 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS v 575 " --> pdb=" O CYS v 571 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS v 576 " --> pdb=" O HIS v 572 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA v 577 " --> pdb=" O ILE v 573 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU v 578 " --> pdb=" O TYR v 574 " (cutoff:3.500A) Processing helix chain 'v' and resid 581 through 593 removed outlier: 3.705A pdb=" N ALA v 585 " --> pdb=" O ARG v 581 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET v 589 " --> pdb=" O ALA v 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU v 590 " --> pdb=" O ARG v 586 " (cutoff:3.500A) Processing helix chain 'v' and resid 594 through 602 removed outlier: 4.502A pdb=" N GLN v 599 " --> pdb=" O GLN v 595 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS v 600 " --> pdb=" O ASP v 596 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP v 602 " --> pdb=" O ILE v 598 " (cutoff:3.500A) Processing helix chain 'v' and resid 603 through 624 removed outlier: 3.996A pdb=" N ILE v 607 " --> pdb=" O PRO v 603 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN v 615 " --> pdb=" O ARG v 611 " (cutoff:3.500A) Processing helix chain 'v' and resid 627 through 638 removed outlier: 4.071A pdb=" N ASP v 635 " --> pdb=" O ASN v 631 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE v 636 " --> pdb=" O ALA v 632 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 647 Processing helix chain 'v' and resid 659 through 670 removed outlier: 3.534A pdb=" N LYS v 664 " --> pdb=" O GLN v 660 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL v 665 " --> pdb=" O GLU v 661 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU v 666 " --> pdb=" O GLN v 662 " (cutoff:3.500A) Processing helix chain 'v' and resid 678 through 699 removed outlier: 3.730A pdb=" N LEU v 692 " --> pdb=" O VAL v 688 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU v 693 " --> pdb=" O SER v 689 " (cutoff:3.500A) Proline residue: v 696 - end of helix Processing helix chain 'v' and resid 713 through 723 removed outlier: 4.076A pdb=" N GLY v 721 " --> pdb=" O GLN v 717 " (cutoff:3.500A) Processing helix chain 'v' and resid 732 through 747 Processing helix chain 'v' and resid 748 through 764 removed outlier: 4.184A pdb=" N CYS v 752 " --> pdb=" O ASP v 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER v 754 " --> pdb=" O LYS v 750 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE v 755 " --> pdb=" O THR v 751 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS v 760 " --> pdb=" O ILE v 756 " (cutoff:3.500A) Processing helix chain 'v' and resid 771 through 800 removed outlier: 3.843A pdb=" N THR v 777 " --> pdb=" O ASP v 773 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS v 782 " --> pdb=" O MET v 778 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU v 788 " --> pdb=" O GLN v 784 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR v 794 " --> pdb=" O THR v 790 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER v 797 " --> pdb=" O PHE v 793 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL v 798 " --> pdb=" O THR v 794 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP v 800 " --> pdb=" O SER v 796 " (cutoff:3.500A) Processing helix chain 'v' and resid 803 through 812 removed outlier: 3.906A pdb=" N LEU v 807 " --> pdb=" O SER v 803 " (cutoff:3.500A) Processing helix chain 'v' and resid 814 through 828 Processing helix chain 'v' and resid 849 through 876 removed outlier: 4.707A pdb=" N GLN v 853 " --> pdb=" O PRO v 849 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA v 856 " --> pdb=" O GLN v 852 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY v 864 " --> pdb=" O ALA v 860 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER v 865 " --> pdb=" O GLU v 861 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU v 866 " --> pdb=" O LYS v 862 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN v 870 " --> pdb=" O LEU v 866 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 14 removed outlier: 3.765A pdb=" N THR w 8 " --> pdb=" O TYR w 4 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG w 9 " --> pdb=" O ASP w 5 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS w 12 " --> pdb=" O THR w 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE w 13 " --> pdb=" O ARG w 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU w 14 " --> pdb=" O ILE w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 32 through 47 removed outlier: 3.822A pdb=" N GLU w 36 " --> pdb=" O TYR w 32 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU w 38 " --> pdb=" O GLU w 34 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN w 39 " --> pdb=" O LYS w 35 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU w 44 " --> pdb=" O GLY w 40 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP w 47 " --> pdb=" O ASP w 43 " (cutoff:3.500A) Processing helix chain 'w' and resid 49 through 60 removed outlier: 7.178A pdb=" N ALA w 54 " --> pdb=" O MET w 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET w 55 " --> pdb=" O VAL w 51 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP w 56 " --> pdb=" O ASP w 52 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL w 57 " --> pdb=" O PHE w 53 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS w 59 " --> pdb=" O MET w 55 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN w 60 " --> pdb=" O ASP w 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 72 Proline residue: w 67 - end of helix removed outlier: 4.229A pdb=" N ARG w 71 " --> pdb=" O PRO w 67 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU w 72 " --> pdb=" O HIS w 68 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 88 removed outlier: 3.988A pdb=" N GLN w 80 " --> pdb=" O THR w 76 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN w 83 " --> pdb=" O ALA w 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU w 84 " --> pdb=" O GLN w 80 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN w 85 " --> pdb=" O LEU w 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR w 88 " --> pdb=" O LEU w 84 " (cutoff:3.500A) Processing helix chain 'w' and resid 94 through 120 Proline residue: w 98 - end of helix removed outlier: 3.621A pdb=" N ARG w 102 " --> pdb=" O PRO w 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN w 105 " --> pdb=" O THR w 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER w 106 " --> pdb=" O ARG w 102 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY w 110 " --> pdb=" O SER w 106 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG w 111 " --> pdb=" O THR w 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU w 113 " --> pdb=" O ASP w 109 " (cutoff:3.500A) Processing helix chain 'w' and resid 124 through 142 removed outlier: 3.602A pdb=" N THR w 130 " --> pdb=" O GLU w 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE w 137 " --> pdb=" O ARG w 133 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU w 140 " --> pdb=" O LYS w 136 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS w 141 " --> pdb=" O PHE w 137 " (cutoff:3.500A) Processing helix chain 'w' and resid 144 through 155 removed outlier: 3.942A pdb=" N ALA w 148 " --> pdb=" O TYR w 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU w 149 " --> pdb=" O SER w 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE w 154 " --> pdb=" O TYR w 150 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG w 155 " --> pdb=" O LEU w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 162 through 180 Processing helix chain 'w' and resid 181 through 199 removed outlier: 3.684A pdb=" N THR w 190 " --> pdb=" O MET w 186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG w 191 " --> pdb=" O GLU w 187 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS w 193 " --> pdb=" O LEU w 189 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU w 194 " --> pdb=" O THR w 190 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN w 199 " --> pdb=" O THR w 195 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 220 removed outlier: 3.992A pdb=" N GLN w 209 " --> pdb=" O LEU w 205 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE w 215 " --> pdb=" O ARG w 211 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP w 217 " --> pdb=" O TRP w 213 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER w 218 " --> pdb=" O LEU w 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU w 219 " --> pdb=" O ILE w 215 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE w 220 " --> pdb=" O HIS w 216 " (cutoff:3.500A) Processing helix chain 'w' and resid 224 through 237 removed outlier: 3.786A pdb=" N GLY w 228 " --> pdb=" O ASN w 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP w 234 " --> pdb=" O ASP w 230 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU w 235 " --> pdb=" O ASN w 231 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE w 236 " --> pdb=" O ILE w 232 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU w 237 " --> pdb=" O ILE w 233 " (cutoff:3.500A) Processing helix chain 'w' and resid 250 through 263 removed outlier: 4.786A pdb=" N LEU w 254 " --> pdb=" O CYS w 250 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG w 255 " --> pdb=" O PRO w 251 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 277 removed outlier: 5.095A pdb=" N ARG w 270 " --> pdb=" O ASP w 266 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG w 271 " --> pdb=" O VAL w 267 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN w 272 " --> pdb=" O ARG w 268 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL w 273 " --> pdb=" O LYS w 269 " (cutoff:3.500A) Processing helix chain 'w' and resid 280 through 290 removed outlier: 3.920A pdb=" N SER w 285 " --> pdb=" O ILE w 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR w 288 " --> pdb=" O GLU w 284 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS w 289 " --> pdb=" O SER w 285 " (cutoff:3.500A) Processing helix chain 'w' and resid 291 through 303 removed outlier: 3.618A pdb=" N GLU w 297 " --> pdb=" O THR w 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU w 299 " --> pdb=" O PHE w 295 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR w 300 " --> pdb=" O VAL w 296 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 322 removed outlier: 3.685A pdb=" N GLU w 316 " --> pdb=" O LEU w 312 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER w 317 " --> pdb=" O ARG w 313 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL w 318 " --> pdb=" O GLU w 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL w 320 " --> pdb=" O GLU w 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN w 321 " --> pdb=" O SER w 317 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP w 322 " --> pdb=" O VAL w 318 " (cutoff:3.500A) Processing helix chain 'w' and resid 328 through 348 removed outlier: 3.547A pdb=" N PHE w 332 " --> pdb=" O CYS w 328 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE w 333 " --> pdb=" O LEU w 329 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG w 337 " --> pdb=" O ILE w 333 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE w 340 " --> pdb=" O ALA w 336 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR w 343 " --> pdb=" O PHE w 339 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE w 347 " --> pdb=" O THR w 343 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS w 348 " --> pdb=" O PHE w 344 " (cutoff:3.500A) Processing helix chain 'w' and resid 352 through 361 Processing helix chain 'w' and resid 363 through 378 Processing helix chain 'w' and resid 400 through 421 removed outlier: 4.831A pdb=" N VAL w 404 " --> pdb=" O PRO w 400 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE w 405 " --> pdb=" O TYR w 401 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU w 406 " --> pdb=" O GLN w 402 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS w 407 " --> pdb=" O GLN w 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS w 409 " --> pdb=" O ILE w 405 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER w 412 " --> pdb=" O THR w 408 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG w 414 " --> pdb=" O SER w 410 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET w 417 " --> pdb=" O PHE w 413 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU w 418 " --> pdb=" O ARG w 414 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA w 419 " --> pdb=" O SER w 415 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 108 removed outlier: 3.731A pdb=" N LEU q 99 " --> pdb=" O HIS q 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER q 105 " --> pdb=" O SER q 101 " (cutoff:3.500A) Processing helix chain 'q' and resid 149 through 164 removed outlier: 3.797A pdb=" N ALA q 153 " --> pdb=" O ASP q 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 180 through 194 removed outlier: 4.007A pdb=" N VAL q 184 " --> pdb=" O THR q 180 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU q 188 " --> pdb=" O VAL q 184 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU q 193 " --> pdb=" O TYR q 189 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 258 removed outlier: 3.997A pdb=" N ARG q 246 " --> pdb=" O TYR q 242 " (cutoff:3.500A) Processing helix chain 'q' and resid 264 through 293 removed outlier: 3.566A pdb=" N GLY q 273 " --> pdb=" O LEU q 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY q 274 " --> pdb=" O GLN q 270 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA q 277 " --> pdb=" O GLY q 273 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU q 291 " --> pdb=" O LEU q 287 " (cutoff:3.500A) Processing helix chain 'q' and resid 297 through 315 removed outlier: 3.563A pdb=" N ASP q 301 " --> pdb=" O LYS q 297 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN q 302 " --> pdb=" O VAL q 298 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR q 303 " --> pdb=" O SER q 299 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL q 304 " --> pdb=" O ALA q 300 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY q 305 " --> pdb=" O ASP q 301 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG q 306 " --> pdb=" O ASN q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 320 through 357 removed outlier: 4.578A pdb=" N GLU q 324 " --> pdb=" O PRO q 320 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU q 352 " --> pdb=" O ILE q 348 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL q 355 " --> pdb=" O ASN q 351 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN q 356 " --> pdb=" O GLU q 352 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 53 removed outlier: 3.597A pdb=" N VAL r 46 " --> pdb=" O ASP r 42 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS r 52 " --> pdb=" O LYS r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 97 through 111 removed outlier: 3.970A pdb=" N VAL r 110 " --> pdb=" O SER r 106 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 145 removed outlier: 3.607A pdb=" N ALA r 143 " --> pdb=" O SER r 139 " (cutoff:3.500A) Processing helix chain 'r' and resid 170 through 177 removed outlier: 3.815A pdb=" N MET r 174 " --> pdb=" O THR r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 184 through 193 removed outlier: 6.125A pdb=" N LYS r 188 " --> pdb=" O PRO r 184 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS r 189 " --> pdb=" O GLU r 185 " (cutoff:3.500A) Processing helix chain 'r' and resid 211 through 224 removed outlier: 3.566A pdb=" N TRP r 216 " --> pdb=" O ASN r 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU r 219 " --> pdb=" O MET r 215 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS r 220 " --> pdb=" O TRP r 216 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA r 223 " --> pdb=" O GLU r 219 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL r 224 " --> pdb=" O LYS r 220 " (cutoff:3.500A) Processing helix chain 'r' and resid 226 through 242 removed outlier: 3.641A pdb=" N SER r 232 " --> pdb=" O HIS r 228 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER r 235 " --> pdb=" O LEU r 231 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER r 236 " --> pdb=" O SER r 232 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN r 237 " --> pdb=" O LEU r 233 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS r 238 " --> pdb=" O ALA r 234 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY r 240 " --> pdb=" O SER r 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS r 241 " --> pdb=" O ASN r 237 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN r 242 " --> pdb=" O HIS r 238 " (cutoff:3.500A) Processing helix chain 'r' and resid 244 through 290 removed outlier: 4.172A pdb=" N VAL r 258 " --> pdb=" O SER r 254 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN r 278 " --> pdb=" O LYS r 274 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN r 279 " --> pdb=" O HIS r 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG r 281 " --> pdb=" O TYR r 277 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG r 288 " --> pdb=" O GLU r 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN r 289 " --> pdb=" O ASN r 285 " (cutoff:3.500A) Processing helix chain 'r' and resid 298 through 304 Processing helix chain 'r' and resid 314 through 352 removed outlier: 3.642A pdb=" N LEU r 318 " --> pdb=" O MET r 314 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN r 322 " --> pdb=" O LEU r 318 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN r 324 " --> pdb=" O ALA r 320 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN r 337 " --> pdb=" O PHE r 333 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU r 338 " --> pdb=" O THR r 334 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY r 339 " --> pdb=" O ALA r 335 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU r 347 " --> pdb=" O MET r 343 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 18 removed outlier: 3.870A pdb=" N GLN s 6 " --> pdb=" O ALA s 2 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN s 10 " --> pdb=" O GLN s 6 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS s 13 " --> pdb=" O ALA s 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS s 16 " --> pdb=" O GLY s 12 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE s 18 " --> pdb=" O LEU s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 25 through 39 removed outlier: 3.514A pdb=" N GLU s 34 " --> pdb=" O GLU s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 58 removed outlier: 3.520A pdb=" N ASN s 47 " --> pdb=" O ASP s 43 " (cutoff:3.500A) Proline residue: s 58 - end of helix Processing helix chain 's' and resid 62 through 77 removed outlier: 3.969A pdb=" N LYS s 72 " --> pdb=" O GLN s 68 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN s 76 " --> pdb=" O LYS s 72 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU s 77 " --> pdb=" O ALA s 73 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 90 removed outlier: 3.733A pdb=" N LYS s 86 " --> pdb=" O PHE s 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS s 87 " --> pdb=" O THR s 83 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET s 88 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP s 90 " --> pdb=" O LYS s 86 " (cutoff:3.500A) Processing helix chain 's' and resid 91 through 96 removed outlier: 4.384A pdb=" N GLU s 95 " --> pdb=" O GLN s 91 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU s 96 " --> pdb=" O ALA s 92 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 91 through 96' Processing helix chain 's' and resid 97 through 112 removed outlier: 7.767A pdb=" N GLN s 101 " --> pdb=" O ARG s 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU s 108 " --> pdb=" O TYR s 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU s 109 " --> pdb=" O LEU s 105 " (cutoff:3.500A) Processing helix chain 's' and resid 113 through 121 Processing helix chain 's' and resid 125 through 131 removed outlier: 3.907A pdb=" N GLU s 129 " --> pdb=" O MET s 125 " (cutoff:3.500A) Processing helix chain 's' and resid 133 through 150 removed outlier: 3.984A pdb=" N ARG s 139 " --> pdb=" O GLU s 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE s 148 " --> pdb=" O HIS s 144 " (cutoff:3.500A) Processing helix chain 's' and resid 154 through 163 Processing helix chain 's' and resid 166 through 178 removed outlier: 3.837A pdb=" N LYS s 171 " --> pdb=" O ASP s 167 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET s 172 " --> pdb=" O SER s 168 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP s 173 " --> pdb=" O GLN s 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY s 178 " --> pdb=" O MET s 174 " (cutoff:3.500A) Processing helix chain 's' and resid 191 through 197 removed outlier: 3.732A pdb=" N ILE s 196 " --> pdb=" O GLN s 192 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS s 197 " --> pdb=" O GLU s 193 " (cutoff:3.500A) Processing helix chain 's' and resid 206 through 215 Processing helix chain 't' and resid 181 through 205 removed outlier: 3.586A pdb=" N GLU t 189 " --> pdb=" O ASP t 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE t 191 " --> pdb=" O ILE t 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN t 193 " --> pdb=" O GLU t 189 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN t 199 " --> pdb=" O GLN t 195 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR t 200 " --> pdb=" O SER t 196 " (cutoff:3.500A) Processing helix chain 't' and resid 208 through 219 removed outlier: 3.824A pdb=" N SER t 217 " --> pdb=" O ASP t 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN t 218 " --> pdb=" O PHE t 214 " (cutoff:3.500A) Proline residue: t 219 - end of helix Processing helix chain 't' and resid 221 through 248 removed outlier: 5.315A pdb=" N HIS t 225 " --> pdb=" O ILE t 221 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU t 228 " --> pdb=" O VAL t 224 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN t 229 " --> pdb=" O HIS t 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL t 230 " --> pdb=" O SER t 226 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU t 234 " --> pdb=" O VAL t 230 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR t 248 " --> pdb=" O LEU t 244 " (cutoff:3.500A) Processing helix chain 't' and resid 251 through 267 removed outlier: 5.064A pdb=" N SER t 255 " --> pdb=" O GLY t 251 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL t 256 " --> pdb=" O ASP t 252 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG t 262 " --> pdb=" O GLY t 258 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS t 263 " --> pdb=" O GLU t 259 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU t 265 " --> pdb=" O GLY t 261 " (cutoff:3.500A) Processing helix chain 't' and resid 273 through 291 removed outlier: 4.965A pdb=" N LEU t 277 " --> pdb=" O SER t 273 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN t 289 " --> pdb=" O GLY t 285 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA t 290 " --> pdb=" O ASP t 286 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE t 291 " --> pdb=" O TYR t 287 " (cutoff:3.500A) Processing helix chain 't' and resid 295 through 304 removed outlier: 3.514A pdb=" N ASN t 300 " --> pdb=" O ASN t 296 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N MET t 304 " --> pdb=" O ASN t 300 " (cutoff:3.500A) Processing helix chain 't' and resid 309 through 327 removed outlier: 3.922A pdb=" N THR t 314 " --> pdb=" O GLU t 310 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR t 318 " --> pdb=" O THR t 314 " (cutoff:3.500A) Processing helix chain 't' and resid 328 through 341 removed outlier: 4.252A pdb=" N ARG t 334 " --> pdb=" O GLN t 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN t 338 " --> pdb=" O ARG t 334 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE t 339 " --> pdb=" O VAL t 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU t 340 " --> pdb=" O PHE t 336 " (cutoff:3.500A) Processing helix chain 't' and resid 356 through 376 removed outlier: 3.620A pdb=" N ILE t 360 " --> pdb=" O LYS t 356 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN t 361 " --> pdb=" O TYR t 357 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN t 364 " --> pdb=" O ILE t 360 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU t 371 " --> pdb=" O MET t 367 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE t 373 " --> pdb=" O ALA t 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA t 374 " --> pdb=" O LEU t 370 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU t 375 " --> pdb=" O LEU t 371 " (cutoff:3.500A) Processing helix chain 't' and resid 381 through 386 removed outlier: 3.728A pdb=" N SER t 385 " --> pdb=" O ARG t 381 " (cutoff:3.500A) Processing helix chain 't' and resid 388 through 403 removed outlier: 4.619A pdb=" N LYS t 393 " --> pdb=" O GLN t 389 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU t 399 " --> pdb=" O GLY t 395 " (cutoff:3.500A) Processing helix chain 't' and resid 406 through 420 removed outlier: 3.876A pdb=" N GLU t 410 " --> pdb=" O PRO t 406 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE t 413 " --> pdb=" O TYR t 409 " (cutoff:3.500A) Proline residue: t 418 - end of helix Processing helix chain 't' and resid 434 through 463 removed outlier: 6.077A pdb=" N GLU t 438 " --> pdb=" O ASN t 434 " (cutoff:3.500A) Proline residue: t 439 - end of helix removed outlier: 4.001A pdb=" N GLN t 442 " --> pdb=" O GLU t 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE t 447 " --> pdb=" O GLN t 443 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP t 449 " --> pdb=" O LYS t 445 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU t 450 " --> pdb=" O VAL t 446 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL t 451 " --> pdb=" O PHE t 447 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN t 453 " --> pdb=" O ASP t 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN t 454 " --> pdb=" O GLU t 450 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN t 456 " --> pdb=" O GLN t 452 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER t 458 " --> pdb=" O GLN t 454 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR t 459 " --> pdb=" O ALA t 455 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE t 460 " --> pdb=" O GLN t 456 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG t 461 " --> pdb=" O LEU t 457 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE t 463 " --> pdb=" O THR t 459 " (cutoff:3.500A) Processing helix chain 't' and resid 471 through 483 removed outlier: 3.541A pdb=" N GLY t 477 " --> pdb=" O ALA t 473 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU t 481 " --> pdb=" O GLY t 477 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU t 483 " --> pdb=" O LEU t 479 " (cutoff:3.500A) Processing helix chain 't' and resid 488 through 500 removed outlier: 3.634A pdb=" N MET t 497 " --> pdb=" O PHE t 493 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS t 498 " --> pdb=" O LYS t 494 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN t 499 " --> pdb=" O HIS t 495 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU t 500 " --> pdb=" O LYS t 496 " (cutoff:3.500A) Processing helix chain 't' and resid 527 through 552 removed outlier: 4.913A pdb=" N ALA t 531 " --> pdb=" O MET t 527 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP t 532 " --> pdb=" O ILE t 528 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS t 534 " --> pdb=" O ILE t 530 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG t 545 " --> pdb=" O ASP t 541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS t 549 " --> pdb=" O ARG t 545 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU t 552 " --> pdb=" O HIS t 548 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 27 removed outlier: 3.974A pdb=" N LEU u 22 " --> pdb=" O LEU u 18 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS u 25 " --> pdb=" O TYR u 21 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 41 removed outlier: 3.664A pdb=" N VAL u 40 " --> pdb=" O GLY u 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP u 41 " --> pdb=" O GLY u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 53 removed outlier: 3.949A pdb=" N ASP u 50 " --> pdb=" O ILE u 46 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL u 51 " --> pdb=" O GLU u 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N CYS u 52 " --> pdb=" O ALA u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 62 through 77 removed outlier: 3.528A pdb=" N LEU u 71 " --> pdb=" O VAL u 67 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU u 72 " --> pdb=" O VAL u 68 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU u 74 " --> pdb=" O LEU u 70 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU u 75 " --> pdb=" O LEU u 71 " (cutoff:3.500A) Proline residue: u 76 - end of helix Processing helix chain 'u' and resid 78 through 94 removed outlier: 3.982A pdb=" N LEU u 82 " --> pdb=" O LYS u 78 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU u 84 " --> pdb=" O GLU u 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU u 86 " --> pdb=" O LEU u 82 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS u 87 " --> pdb=" O ILE u 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS u 89 " --> pdb=" O SER u 85 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU u 90 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL u 91 " --> pdb=" O CYS u 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 107 Proline residue: u 99 - end of helix removed outlier: 4.609A pdb=" N LEU u 106 " --> pdb=" O ARG u 102 " (cutoff:3.500A) Processing helix chain 'u' and resid 117 through 130 removed outlier: 4.450A pdb=" N TYR u 121 " --> pdb=" O THR u 117 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR u 124 " --> pdb=" O ARG u 120 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS u 129 " --> pdb=" O CYS u 125 " (cutoff:3.500A) Processing helix chain 'u' and resid 132 through 150 removed outlier: 3.774A pdb=" N ALA u 136 " --> pdb=" O ALA u 132 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN u 138 " --> pdb=" O CYS u 134 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR u 139 " --> pdb=" O GLY u 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE u 140 " --> pdb=" O ALA u 136 " (cutoff:3.500A) Proline residue: u 141 - end of helix Processing helix chain 'u' and resid 154 through 173 removed outlier: 3.731A pdb=" N THR u 158 " --> pdb=" O TRP u 154 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL u 173 " --> pdb=" O TYR u 169 " (cutoff:3.500A) Processing helix chain 'u' and resid 174 through 192 removed outlier: 3.752A pdb=" N GLU u 187 " --> pdb=" O LYS u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 198 through 215 removed outlier: 4.195A pdb=" N ASP u 203 " --> pdb=" O GLN u 199 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS u 205 " --> pdb=" O ARG u 201 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG u 206 " --> pdb=" O VAL u 202 " (cutoff:3.500A) Proline residue: u 215 - end of helix Processing helix chain 'u' and resid 220 through 227 removed outlier: 3.897A pdb=" N LEU u 226 " --> pdb=" O HIS u 222 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS u 227 " --> pdb=" O LEU u 223 " (cutoff:3.500A) Processing helix chain 'u' and resid 228 through 233 removed outlier: 4.283A pdb=" N GLU u 233 " --> pdb=" O VAL u 229 " (cutoff:3.500A) Processing helix chain 'u' and resid 239 through 250 removed outlier: 4.282A pdb=" N ILE u 243 " --> pdb=" O ASP u 239 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE u 244 " --> pdb=" O LEU u 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS u 248 " --> pdb=" O PHE u 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU u 249 " --> pdb=" O VAL u 245 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA u 250 " --> pdb=" O SER u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 251 through 259 removed outlier: 4.693A pdb=" N PHE u 255 " --> pdb=" O SER u 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR u 256 " --> pdb=" O TYR u 252 " (cutoff:3.500A) Processing helix chain 'u' and resid 260 through 267 removed outlier: 3.718A pdb=" N SER u 265 " --> pdb=" O ASP u 261 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU u 266 " --> pdb=" O PHE u 262 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY u 267 " --> pdb=" O ILE u 263 " (cutoff:3.500A) Processing helix chain 'u' and resid 269 through 289 removed outlier: 4.767A pdb=" N ASN u 273 " --> pdb=" O LEU u 269 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET u 274 " --> pdb=" O HIS u 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE u 282 " --> pdb=" O ARG u 278 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL u 287 " --> pdb=" O MET u 283 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN u 289 " --> pdb=" O MET u 285 " (cutoff:3.500A) Processing helix chain 'u' and resid 293 through 302 removed outlier: 3.729A pdb=" N MET u 297 " --> pdb=" O SER u 293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN u 298 " --> pdb=" O PHE u 294 " (cutoff:3.500A) Processing helix chain 'u' and resid 304 through 319 removed outlier: 3.816A pdb=" N VAL u 308 " --> pdb=" O GLY u 304 " (cutoff:3.500A) Processing helix chain 'u' and resid 341 through 370 removed outlier: 3.779A pdb=" N ASP u 352 " --> pdb=" O GLN u 348 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR u 353 " --> pdb=" O GLN u 349 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP u 357 " --> pdb=" O THR u 353 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS u 358 " --> pdb=" O LEU u 354 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN u 362 " --> pdb=" O LYS u 358 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS u 363 " --> pdb=" O GLN u 359 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS u 365 " --> pdb=" O LEU u 361 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU u 368 " --> pdb=" O VAL u 364 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 24 through 28 removed outlier: 5.501A pdb=" N HIS C 24 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 28 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY C 45 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 96 through 100 removed outlier: 3.701A pdb=" N THR C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 78 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 75 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 123 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 44 through 48 removed outlier: 3.828A pdb=" N GLY D 45 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR D 47 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.365A pdb=" N HIS D 101 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 217 " --> pdb=" O HIS D 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 214 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 134 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D 123 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 143 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR D 119 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 139 through 142 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'E' and resid 88 through 92 removed outlier: 3.708A pdb=" N LYS E 88 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE E 112 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 168 through 172 removed outlier: 3.646A pdb=" N GLY E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 210 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA E 183 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP E 206 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS E 207 " --> pdb=" O GLY E 188 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR E 209 " --> pdb=" O ILE E 190 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 109 through 116 Processing sheet with id= 9, first strand: chain 'F' and resid 45 through 53 removed outlier: 3.516A pdb=" N ILE F 48 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 89 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL F 91 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 148 through 155 removed outlier: 4.412A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 185 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY F 180 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 89 through 93 removed outlier: 3.804A pdb=" N ILE G 90 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 121 through 126 removed outlier: 4.586A pdb=" N ASP G 158 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR G 159 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.722A pdb=" N LYS G 128 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE G 130 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 180 through 184 removed outlier: 6.894A pdb=" N LEU G 180 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN G 224 " --> pdb=" O THR G 184 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 197 through 200 removed outlier: 4.661A pdb=" N ASN G 197 " --> pdb=" O HIS G 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS G 209 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL G 207 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 123 through 128 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'I' and resid 11 through 17 removed outlier: 3.593A pdb=" N ILE I 16 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU I 109 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN I 110 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 52 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR I 34 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 159 through 163 removed outlier: 3.668A pdb=" N ARG I 170 " --> pdb=" O LEU I 162 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 54 through 57 removed outlier: 4.068A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 47 through 53 removed outlier: 4.619A pdb=" N ALA J 47 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG J 57 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL J 93 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 62 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL J 64 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 140 through 147 removed outlier: 4.363A pdb=" N SER J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP J 184 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 154 " --> pdb=" O ASP J 184 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= 23, first strand: chain 'K' and resid 71 through 75 removed outlier: 3.544A pdb=" N ARG K 74 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER K 66 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY K 68 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP K 186 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU K 171 " --> pdb=" O ILE K 104 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS K 100 " --> pdb=" O ILE K 175 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.762A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 71 through 75 removed outlier: 5.772A pdb=" N ARG N 71 " --> pdb=" O GLU N 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 126 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR N 127 " --> pdb=" O LEU N 143 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 85 through 95 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.874A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 30 through 33 removed outlier: 5.735A pdb=" N GLY O 30 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS O 112 " --> pdb=" O GLY O 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL O 110 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER O 107 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN O 75 " --> pdb=" O HIS O 48 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS O 50 " --> pdb=" O ASN O 75 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER O 54 " --> pdb=" O VAL O 79 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 51 through 55 removed outlier: 6.760A pdb=" N GLU Q 51 " --> pdb=" O ASP Q 46 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL Q 44 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG Q 55 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL Q 42 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE Q 41 " --> pdb=" O PHE Q 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS Q 43 " --> pdb=" O HIS Q 32 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS Q 32 " --> pdb=" O HIS Q 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL Q 30 " --> pdb=" O THR Q 45 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS Q 96 " --> pdb=" O CYS Q 31 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE Q 95 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.629A pdb=" N GLU Q 130 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU Q 97 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL Q 132 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA Q 99 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 9 through 15 removed outlier: 3.730A pdb=" N ARG S 69 " --> pdb=" O HIS S 24 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU S 31 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE S 68 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL S 70 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'W' and resid 56 through 66 removed outlier: 5.628A pdb=" N LYS W 86 " --> pdb=" O PRO W 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS W 59 " --> pdb=" O ILE W 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 84 " --> pdb=" O LYS W 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR W 65 " --> pdb=" O ASP W 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 21 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'X' and resid 32 through 37 removed outlier: 3.569A pdb=" N MET X 34 " --> pdb=" O TYR X 53 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Y' and resid 23 through 28 removed outlier: 5.337A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU Y 65 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL Y 25 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL Y 63 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU Y 49 " --> pdb=" O ASN Y 64 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Z' and resid 46 through 49 removed outlier: 3.776A pdb=" N ALA Z 47 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU Z 101 " --> pdb=" O VAL Z 123 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Z' and resid 53 through 59 removed outlier: 5.941A pdb=" N VAL Z 57 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA Z 65 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS Z 79 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'a' and resid 5 through 8 Processing sheet with id= 38, first strand: chain 'a' and resid 20 through 29 removed outlier: 3.910A pdb=" N HIS a 29 " --> pdb=" O GLY a 67 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY a 67 " --> pdb=" O HIS a 29 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'b' and resid 20 through 24 removed outlier: 4.246A pdb=" N CYS b 28 " --> pdb=" O CYS b 23 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.783A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 32 through 35 removed outlier: 4.084A pdb=" N ARG c 81 " --> pdb=" O PHE c 32 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP c 34 " --> pdb=" O PHE c 79 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'd' and resid 9 through 14 removed outlier: 3.841A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP d 54 " --> pdb=" O VAL d 14 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'd' and resid 18 through 22 removed outlier: 3.674A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE d 34 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ARG d 40 " --> pdb=" O PHE d 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'f' and resid 137 through 140 removed outlier: 6.758A pdb=" N ASP f 137 " --> pdb=" O LYS f 152 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS f 152 " --> pdb=" O ASP f 137 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 5 through 12 removed outlier: 4.730A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR g 302 " --> pdb=" O LEU g 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN g 296 " --> pdb=" O VAL g 312 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR g 297 " --> pdb=" O SER g 292 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'g' and resid 20 through 23 removed outlier: 4.185A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP g 29 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU g 45 " --> pdb=" O ASP g 29 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR g 46 " --> pdb=" O TYR g 52 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR g 52 " --> pdb=" O THR g 46 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.184A pdb=" N PHE g 77 " --> pdb=" O SER g 72 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG g 88 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU g 87 " --> pdb=" O PHE g 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 109 through 114 removed outlier: 3.862A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN g 119 " --> pdb=" O SER g 114 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER g 124 " --> pdb=" O THR g 128 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 153 through 157 removed outlier: 5.368A pdb=" N ILE g 164 " --> pdb=" O SER g 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU g 179 " --> pdb=" O PRO g 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 176 " --> pdb=" O THR g 186 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 196 through 201 removed outlier: 3.553A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER g 201 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU g 206 " --> pdb=" O SER g 201 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY g 214 " --> pdb=" O GLY g 232 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 238 through 242 removed outlier: 4.493A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER g 242 " --> pdb=" O TRP g 247 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TRP g 247 " --> pdb=" O SER g 242 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER g 255 " --> pdb=" O THR g 252 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 39 through 42 removed outlier: 3.502A pdb=" N ILE g 40 " --> pdb=" O LEU g 59 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= 54, first strand: chain 'A' and resid 32 through 36 removed outlier: 5.089A pdb=" N ILE A 42 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'A' and resid 225 through 229 Processing sheet with id= 56, first strand: chain 'B' and resid 116 through 119 Processing sheet with id= 57, first strand: chain 'B' and resid 137 through 140 removed outlier: 7.292A pdb=" N ILE B 101 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS B 93 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 97 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 55 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 148 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY B 61 " --> pdb=" O CYS B 148 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 268 through 272 removed outlier: 6.939A pdb=" N LEU B 269 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL B 370 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 271 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B' and resid 290 through 295 Processing sheet with id= 60, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.981A pdb=" N GLY B 299 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B' and resid 305 through 310 removed outlier: 4.711A pdb=" N GLN B 305 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N MET B 323 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.893A pdb=" N GLU B 379 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'B' and resid 424 through 429 removed outlier: 3.586A pdb=" N MET B 418 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 385 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR B 388 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP B 436 " --> pdb=" O TYR B 388 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 32 through 37 removed outlier: 6.515A pdb=" N GLY j 32 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU j 78 " --> pdb=" O ILE j 92 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN j 87 " --> pdb=" O LYS j 56 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL j 55 " --> pdb=" O CYS j 51 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG j 57 " --> pdb=" O ALA j 49 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA j 49 " --> pdb=" O ARG j 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 6 through 11 Processing sheet with id= 66, first strand: chain 'k' and resid 38 through 41 removed outlier: 7.434A pdb=" N CYS k 38 " --> pdb=" O SER k 51 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 92 through 95 removed outlier: 3.553A pdb=" N HIS k 95 " --> pdb=" O GLY k 297 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 166 through 169 removed outlier: 4.344A pdb=" N ILE k 167 " --> pdb=" O ILE k 237 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP k 241 " --> pdb=" O LYS k 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE k 238 " --> pdb=" O TYR k 268 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU k 104 " --> pdb=" O ARG k 267 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE k 269 " --> pdb=" O GLU k 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE k 285 " --> pdb=" O VAL k 105 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 351 through 356 removed outlier: 3.800A pdb=" N VAL k 365 " --> pdb=" O ALA k 545 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL k 534 " --> pdb=" O ASN k 546 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'k' and resid 374 through 377 removed outlier: 3.894A pdb=" N THR k 514 " --> pdb=" O ASP k 481 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP k 486 " --> pdb=" O LYS k 412 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 565 through 570 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.345A pdb=" N HIS U 11 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY U 22 " --> pdb=" O HIS U 11 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'R' and resid 75 through 78 Processing sheet with id= 74, first strand: chain 'm' and resid 190 through 193 removed outlier: 4.341A pdb=" N GLN m 191 " --> pdb=" O ARG m 362 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR m 360 " --> pdb=" O ILE m 193 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'm' and resid 390 through 399 removed outlier: 3.871A pdb=" N ASN m 392 " --> pdb=" O TYR m 446 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS m 394 " --> pdb=" O LYS m 448 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR m 451 " --> pdb=" O LEU m 466 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 504 through 511 removed outlier: 4.157A pdb=" N TRP m 265 " --> pdb=" O LYS m 510 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA m 247 " --> pdb=" O ILE m 372 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'm' and resid 356 through 360 removed outlier: 3.968A pdb=" N ALA m 357 " --> pdb=" O HIS m 377 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS m 377 " --> pdb=" O ALA m 357 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'v' and resid 833 through 837 Processing sheet with id= 79, first strand: chain 'w' and resid 382 through 385 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain 'q' and resid 117 through 121 removed outlier: 4.351A pdb=" N LEU q 120 " --> pdb=" O GLY q 171 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY q 171 " --> pdb=" O LEU q 120 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE q 213 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL q 237 " --> pdb=" O ILE q 213 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA q 215 " --> pdb=" O LEU q 235 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU q 235 " --> pdb=" O ALA q 215 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL q 217 " --> pdb=" O THR q 233 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET q 231 " --> pdb=" O THR q 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL q 129 " --> pdb=" O VAL q 91 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'r' and resid 37 through 41 removed outlier: 3.689A pdb=" N GLN r 38 " --> pdb=" O ASP r 74 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'r' and resid 64 through 67 removed outlier: 3.546A pdb=" N GLY r 118 " --> pdb=" O LEU r 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP r 119 " --> pdb=" O VAL r 148 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN r 121 " --> pdb=" O LEU r 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR r 152 " --> pdb=" O GLN r 121 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR r 167 " --> pdb=" O VAL r 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER r 163 " --> pdb=" O ASP r 153 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 's' and resid 179 through 182 removed outlier: 4.242A pdb=" N SER s 180 " --> pdb=" O PHE s 188 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN s 186 " --> pdb=" O ASP s 182 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 't' and resid 503 through 508 removed outlier: 5.088A pdb=" N THR t 503 " --> pdb=" O ALA t 516 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU t 512 " --> pdb=" O SER t 507 " (cutoff:3.500A) 2914 hydrogen bonds defined for protein. 8673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1258 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 504 basepair parallelities 888 stacking parallelities Total time for adding SS restraints: 71.51 Time building geometry restraints manager: 44.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.95: 7 0.95 - 1.46: 70151 1.46 - 1.97: 54442 1.97 - 2.48: 32 2.48 - 2.98: 4 Warning: very small bond lengths. Bond restraints: 124636 Sorted by residual: bond pdb=" C ASP k 521 " pdb=" N PHE k 522 " ideal model delta sigma weight residual 1.335 2.984 -1.649 1.25e-02 6.40e+03 1.74e+04 bond pdb=" C ARG U 142 " pdb=" N GLY U 143 " ideal model delta sigma weight residual 1.329 2.920 -1.591 1.40e-02 5.10e+03 1.29e+04 bond pdb=" C ILE k 451 " pdb=" N GLU k 452 " ideal model delta sigma weight residual 1.332 2.788 -1.456 1.40e-02 5.10e+03 1.08e+04 bond pdb=" C GLU k 373 " pdb=" N ILE k 374 " ideal model delta sigma weight residual 1.329 2.703 -1.374 1.63e-02 3.76e+03 7.11e+03 bond pdb=" C THR k 550 " pdb=" N LEU k 551 " ideal model delta sigma weight residual 1.335 2.350 -1.015 1.27e-02 6.20e+03 6.39e+03 ... (remaining 124631 not shown) Histogram of bond angle deviations from ideal: 35.70 - 64.31: 6 64.31 - 92.93: 57 92.93 - 121.54: 141801 121.54 - 150.15: 35369 150.15 - 178.77: 5 Bond angle restraints: 177238 Sorted by residual: angle pdb=" C ARG k 531 " pdb=" N VAL k 532 " pdb=" CA VAL k 532 " ideal model delta sigma weight residual 122.37 35.70 86.67 1.29e+00 6.01e-01 4.51e+03 angle pdb=" O LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 122.12 178.77 -56.65 1.06e+00 8.90e-01 2.86e+03 angle pdb=" CA ARG k 531 " pdb=" C ARG k 531 " pdb=" N VAL k 532 " ideal model delta sigma weight residual 116.37 43.39 72.98 1.45e+00 4.76e-01 2.53e+03 angle pdb=" CA LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 117.30 61.23 56.07 1.16e+00 7.43e-01 2.34e+03 angle pdb=" CA ASN v 762 " pdb=" C ASN v 762 " pdb=" N GLY v 763 " ideal model delta sigma weight residual 117.30 64.77 52.53 1.16e+00 7.43e-01 2.05e+03 ... (remaining 177233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 72115 35.99 - 71.99: 4130 71.99 - 107.98: 605 107.98 - 143.97: 24 143.97 - 179.96: 30 Dihedral angle restraints: 76904 sinusoidal: 48365 harmonic: 28539 Sorted by residual: dihedral pdb=" CA SER r 122 " pdb=" C SER r 122 " pdb=" N THR r 123 " pdb=" CA THR r 123 " ideal model delta harmonic sigma weight residual -180.00 -48.38 -131.62 0 5.00e+00 4.00e-02 6.93e+02 dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 48.40 131.60 0 5.00e+00 4.00e-02 6.93e+02 dihedral pdb=" CA ASN j 19 " pdb=" C ASN j 19 " pdb=" N GLU j 20 " pdb=" CA GLU j 20 " ideal model delta harmonic sigma weight residual 180.00 53.27 126.73 0 5.00e+00 4.00e-02 6.42e+02 ... (remaining 76901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 21331 1.005 - 2.010: 6 2.010 - 3.015: 0 3.015 - 4.020: 1 4.020 - 5.025: 3 Chirality restraints: 21341 Sorted by residual: chirality pdb=" C4' C4J 21244 " pdb=" C5' C4J 21244 " pdb=" O4' C4J 21244 " pdb=" C3' C4J 21244 " both_signs ideal model delta sigma weight residual False 2.50 -2.53 5.02 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C2' C 1 17 " pdb=" C3' C 1 17 " pdb=" O2' C 1 17 " pdb=" C1' C 1 17 " both_signs ideal model delta sigma weight residual False -2.52 2.05 -4.57 2.00e-01 2.50e+01 5.22e+02 chirality pdb=" C3' G 1 18 " pdb=" C4' G 1 18 " pdb=" O3' G 1 18 " pdb=" C2' G 1 18 " both_signs ideal model delta sigma weight residual False -2.48 1.89 -4.37 2.00e-01 2.50e+01 4.77e+02 ... (remaining 21338 not shown) Planarity restraints: 15674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE k 451 " -0.184 2.00e-02 2.50e+03 2.66e-01 7.05e+02 pdb=" C ILE k 451 " 0.440 2.00e-02 2.50e+03 pdb=" O ILE k 451 " -0.232 2.00e-02 2.50e+03 pdb=" N GLU k 452 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU k 378 " -0.080 2.00e-02 2.50e+03 2.25e-01 5.08e+02 pdb=" C LEU k 378 " 0.379 2.00e-02 2.50e+03 pdb=" O LEU k 378 " -0.216 2.00e-02 2.50e+03 pdb=" N GLY k 379 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU y 245 " -0.099 2.00e-02 2.50e+03 1.92e-01 3.69e+02 pdb=" C LEU y 245 " 0.331 2.00e-02 2.50e+03 pdb=" O LEU y 245 " -0.136 2.00e-02 2.50e+03 pdb=" N TRP y 246 " -0.097 2.00e-02 2.50e+03 ... (remaining 15671 not shown) Histogram of nonbonded interaction distances: 0.63 - 1.49: 63 1.49 - 2.34: 485 2.34 - 3.19: 98990 3.19 - 4.05: 325698 4.05 - 4.90: 549186 Warning: very small nonbonded interaction distances. Nonbonded interactions: 974422 Sorted by model distance: nonbonded pdb=" NE2 HIS v 736 " pdb=" OE1 GLU v 759 " model vdw 0.634 2.520 nonbonded pdb=" CH2 TRP y 284 " pdb=" NE2 GLN y 426 " model vdw 0.727 3.420 nonbonded pdb=" C ILE k 451 " pdb=" N ASN k 453 " model vdw 0.805 3.350 nonbonded pdb=" CZ ARG y 367 " pdb=" CE1 HIS y 510 " model vdw 0.823 3.490 nonbonded pdb=" NH2 ARG y 367 " pdb=" CE1 HIS y 510 " model vdw 0.831 3.340 ... (remaining 974417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.97 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: 1.830 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: 0.090 Extract box with map and model: 16.430 Check model and map are aligned: 1.260 Set scattering table: 0.830 Process input model: 330.310 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 355.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 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 : 0.021 1.649 124636 Z= 1.361 Angle : 2.064 86.669 177238 Z= 1.288 Chirality : 0.118 5.025 21341 Planarity : 0.018 0.522 15674 Dihedral : 19.489 179.965 58441 Min Nonbonded Distance : 0.634 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 4.00 % Allowed : 10.80 % Favored : 85.20 % Rotamer: Outliers : 3.01 % Allowed : 5.49 % Favored : 91.50 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.47 % Twisted Proline : 4.89 % Twisted General : 1.52 % 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: -4.49 (0.07), residues: 9695 helix: -3.06 (0.06), residues: 3625 sheet: -2.46 (0.14), residues: 1114 loop : -3.06 (0.08), residues: 4956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.013 TRP s 173 HIS 0.013 0.001 HIS A 11 PHE 0.154 0.010 PHE k 535 TYR 0.253 0.016 TYR v 583 ARG 0.028 0.001 ARG k 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2367 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 2108 time to evaluate : 7.401 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 outliers start: 259 outliers final: 46 residues processed: 2313 average time/residue: 1.1743 time to fit residues: 4466.7985 Evaluate side-chains 1170 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1124 time to evaluate : 7.479 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 5 residues processed: 46 average time/residue: 0.9838 time to fit residues: 89.8554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 0.9980 chunk 867 optimal weight: 8.9990 chunk 481 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 585 optimal weight: 5.9990 chunk 463 optimal weight: 5.9990 chunk 897 optimal weight: 0.0570 chunk 347 optimal weight: 6.9990 chunk 545 optimal weight: 0.8980 chunk 667 optimal weight: 5.9990 chunk 1039 optimal weight: 8.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 169 HIS D 136 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 220 ASN E 257 HIS F 4 GLN F 74 GLN G 8 HIS G 17 HIS G 98 ASN H 74 ASN H 203 ASN J 91 HIS ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 GLN L 27 GLN M 84 HIS P 90 HIS Q 32 HIS T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 5 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 GLN Z 16 HIS Z 31 HIS Z 61 GLN b 72 HIS c 51 GLN c 65 GLN e 10 HIS f 111 ASN g 117 ASN g 159 ASN g 187 ASN g 196 ASN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN A 169 ASN j 37 GLN j 60 HIS ** k 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 154 ASN ** k 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS k 546 ASN k 556 ASN k 588 GLN k 593 ASN U 85 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 296 ASN m 377 HIS m 479 GLN m 486 ASN m 515 GLN y 10 ASN y 73 GLN y 122 GLN y 179 GLN y 187 GLN ** y 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 301 HIS y 430 GLN ** y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 377 ASN v 399 GLN v 472 HIS v 674 HIS ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 819 HIS v 858 GLN w 80 GLN w 138 GLN w 252 HIS w 264 ASN w 348 HIS w 390 HIS ** q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 182 HIS q 260 ASN q 288 GLN q 345 GLN r 40 GLN r 54 GLN r 58 GLN r 87 HIS ** r 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 141 GLN r 212 ASN r 237 ASN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN t 232 HIS t 281 HIS t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 389 GLN t 442 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 33 ASN u 298 GLN u 345 GLN u 360 ASN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 124636 Z= 0.224 Angle : 0.801 15.742 177238 Z= 0.411 Chirality : 0.043 0.445 21341 Planarity : 0.006 0.156 15674 Dihedral : 20.367 178.583 38303 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.33 % Favored : 90.86 % Rotamer: Outliers : 3.24 % Allowed : 12.04 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 3.53 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.08), residues: 9717 helix: -1.26 (0.08), residues: 3797 sheet: -1.67 (0.14), residues: 1186 loop : -2.83 (0.08), residues: 4734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 192 HIS 0.042 0.002 HIS y 297 PHE 0.040 0.002 PHE v 755 TYR 0.031 0.002 TYR k 527 ARG 0.010 0.001 ARG j 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1310 time to evaluate : 7.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 279 outliers final: 111 residues processed: 1488 average time/residue: 1.0926 time to fit residues: 2791.5812 Evaluate side-chains 1101 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 990 time to evaluate : 7.434 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 0.8607 time to fit residues: 192.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 20.0000 chunk 322 optimal weight: 1.9990 chunk 865 optimal weight: 6.9990 chunk 708 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 1041 optimal weight: 10.0000 chunk 1125 optimal weight: 9.9990 chunk 927 optimal weight: 5.9990 chunk 1032 optimal weight: 30.0000 chunk 355 optimal weight: 4.9990 chunk 835 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 179 ASN F 57 ASN G 50 ASN G 67 GLN G 142 HIS H 203 ASN I 155 GLN J 76 GLN K 7 ASN K 64 ASN ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN L 113 GLN M 32 HIS N 13 GLN N 83 GLN N 94 HIS ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 HIS P 58 HIS S 48 GLN T 118 GLN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 HIS Z 77 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN b 17 HIS b 80 HIS c 65 GLN d 29 GLN g 104 HIS g 226 HIS n 106 GLN n 112 ASN i 113 ASN i 132 ASN k 78 ASN k 85 HIS ** k 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 542 ASN U 87 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 321 HIS m 377 HIS ** y 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 292 HIS y 434 ASN y 466 GLN y 477 HIS v 430 ASN v 509 HIS v 579 HIS v 595 GLN ** v 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 717 GLN ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 858 GLN w 396 ASN ** q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 271 GLN ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 109 HIS ** r 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 242 ASN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 489 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 222 HIS u 238 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 124636 Z= 0.318 Angle : 0.834 15.728 177238 Z= 0.429 Chirality : 0.046 0.503 21341 Planarity : 0.007 0.146 15674 Dihedral : 20.371 178.606 38303 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.98 % Favored : 89.41 % Rotamer: Outliers : 3.22 % Allowed : 15.00 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 2.72 % Twisted General : 0.42 % 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: -2.64 (0.08), residues: 9717 helix: -0.77 (0.08), residues: 3841 sheet: -1.16 (0.14), residues: 1246 loop : -2.83 (0.08), residues: 4630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP y 393 HIS 0.026 0.002 HIS y 297 PHE 0.044 0.003 PHE g 113 TYR 0.033 0.003 TYR e 46 ARG 0.026 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1209 time to evaluate : 7.525 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 outliers start: 277 outliers final: 132 residues processed: 1402 average time/residue: 1.0516 time to fit residues: 2531.8360 Evaluate side-chains 1084 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 952 time to evaluate : 7.464 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 0 residues processed: 132 average time/residue: 0.8493 time to fit residues: 221.4898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1029 optimal weight: 7.9990 chunk 783 optimal weight: 8.9990 chunk 540 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 699 optimal weight: 6.9990 chunk 1045 optimal weight: 0.6980 chunk 1106 optimal weight: 0.6980 chunk 546 optimal weight: 10.0000 chunk 990 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 98 GLN F 179 GLN G 201 HIS I 65 GLN I 155 GLN J 76 GLN K 7 ASN ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 HIS Q 103 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 HIS ** a 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN c 65 GLN g 147 HIS g 285 GLN j 85 GLN k 251 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 469 GLN ** y 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS y 522 GLN v 377 ASN v 509 HIS v 610 ASN ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 637 GLN v 674 HIS ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 143 ASN w 241 GLN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 271 GLN q 345 GLN r 121 GLN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 324 ASN ** r 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 344 GLN t 363 GLN t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 402 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 33 ASN u 327 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 124636 Z= 0.262 Angle : 0.751 17.251 177238 Z= 0.385 Chirality : 0.043 0.281 21341 Planarity : 0.006 0.170 15674 Dihedral : 20.308 179.807 38303 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.32 % Favored : 90.15 % Rotamer: Outliers : 2.96 % Allowed : 17.24 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.51 % Twisted Proline : 1.90 % Twisted General : 0.24 % 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: -2.37 (0.08), residues: 9717 helix: -0.45 (0.08), residues: 3843 sheet: -1.01 (0.14), residues: 1255 loop : -2.79 (0.08), residues: 4619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP m 363 HIS 0.015 0.002 HIS y 297 PHE 0.040 0.002 PHE g 113 TYR 0.032 0.002 TYR S 99 ARG 0.020 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1097 time to evaluate : 7.495 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 outliers start: 255 outliers final: 118 residues processed: 1271 average time/residue: 1.0588 time to fit residues: 2325.9947 Evaluate side-chains 1058 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 940 time to evaluate : 7.499 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 0 residues processed: 118 average time/residue: 0.9008 time to fit residues: 211.1320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 921 optimal weight: 20.0000 chunk 628 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 824 optimal weight: 30.0000 chunk 456 optimal weight: 7.9990 chunk 944 optimal weight: 7.9990 chunk 765 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 565 optimal weight: 10.0000 chunk 993 optimal weight: 30.0000 chunk 279 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN G 112 HIS I 105 ASN I 155 GLN J 76 GLN K 7 ASN K 167 GLN K 181 GLN N 65 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN Q 103 ASN S 8 GLN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 HIS a 89 HIS a 124 ASN c 9 HIS c 65 GLN ** e 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS i 111 GLN A 114 HIS k 95 HIS ** k 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 408 ASN k 468 GLN k 593 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 322 ASN m 428 ASN y 211 HIS v 377 ASN v 415 ASN v 433 ASN v 436 GLN v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 60 ASN w 198 ASN w 209 GLN ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 244 ASN w 395 ASN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 228 HIS r 272 GLN ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN s 76 ASN t 239 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 442 GLN t 489 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 349 GLN u 355 ASN u 366 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.190 124636 Z= 0.413 Angle : 0.964 16.605 177238 Z= 0.490 Chirality : 0.051 0.309 21341 Planarity : 0.008 0.159 15674 Dihedral : 20.771 179.648 38303 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.47 % Favored : 87.95 % Rotamer: Outliers : 4.02 % Allowed : 18.81 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 1.90 % Twisted General : 0.29 % 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: -2.84 (0.08), residues: 9717 helix: -0.90 (0.08), residues: 3805 sheet: -1.07 (0.14), residues: 1228 loop : -3.04 (0.08), residues: 4684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP m 363 HIS 0.014 0.003 HIS f 93 PHE 0.073 0.004 PHE k 324 TYR 0.040 0.003 TYR k 316 ARG 0.030 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1088 time to evaluate : 6.718 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 outliers start: 346 outliers final: 166 residues processed: 1333 average time/residue: 1.0270 time to fit residues: 2367.3580 Evaluate side-chains 1121 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 955 time to evaluate : 7.591 Switching outliers to nearest non-outliers outliers start: 166 outliers final: 0 residues processed: 166 average time/residue: 0.8594 time to fit residues: 277.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 7.9990 chunk 996 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 649 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 1107 optimal weight: 7.9990 chunk 919 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 581 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 179 GLN F 207 HIS I 155 GLN J 168 HIS K 167 GLN N 65 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 10 HIS g 311 GLN A 23 ASN A 68 ASN ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN k 408 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 869 ASN w 39 GLN ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 489 GLN ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 355 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 124636 Z= 0.273 Angle : 0.774 17.696 177238 Z= 0.396 Chirality : 0.044 0.307 21341 Planarity : 0.006 0.171 15674 Dihedral : 20.551 179.126 38303 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.25 % Favored : 89.28 % Rotamer: Outliers : 2.23 % Allowed : 21.19 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 1.63 % Twisted General : 0.22 % 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: -2.53 (0.08), residues: 9717 helix: -0.56 (0.08), residues: 3829 sheet: -0.94 (0.14), residues: 1216 loop : -2.93 (0.08), residues: 4672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 152 HIS 0.018 0.002 HIS q 95 PHE 0.035 0.002 PHE w 53 TYR 0.031 0.002 TYR v 799 ARG 0.011 0.001 ARG y 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1032 time to evaluate : 7.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 192 outliers final: 97 residues processed: 1164 average time/residue: 1.0741 time to fit residues: 2171.5747 Evaluate side-chains 1044 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 947 time to evaluate : 7.563 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.8680 time to fit residues: 170.3188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1068 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 631 optimal weight: 5.9990 chunk 809 optimal weight: 0.9990 chunk 626 optimal weight: 20.0000 chunk 932 optimal weight: 0.8980 chunk 618 optimal weight: 20.0000 chunk 1103 optimal weight: 30.0000 chunk 690 optimal weight: 4.9990 chunk 672 optimal weight: 10.0000 chunk 509 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN I 155 GLN J 76 GLN J 168 HIS K 167 GLN N 65 ASN N 141 ASN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 187 ASN g 226 HIS ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN k 127 GLN U 11 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 270 GLN ** v 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 467 GLN v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 209 GLN ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 309 GLN w 349 GLN ** q 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 360 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 124636 Z= 0.243 Angle : 0.733 14.681 177238 Z= 0.375 Chirality : 0.042 0.302 21341 Planarity : 0.006 0.161 15674 Dihedral : 20.467 179.459 38303 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.99 % Favored : 88.55 % Rotamer: Outliers : 1.85 % Allowed : 21.78 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.21 % 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: -2.32 (0.08), residues: 9717 helix: -0.30 (0.08), residues: 3826 sheet: -0.90 (0.14), residues: 1222 loop : -2.87 (0.08), residues: 4669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 152 HIS 0.009 0.001 HIS j 60 PHE 0.065 0.002 PHE w 53 TYR 0.055 0.002 TYR v 791 ARG 0.011 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1021 time to evaluate : 7.125 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 outliers start: 159 outliers final: 82 residues processed: 1113 average time/residue: 1.0468 time to fit residues: 2016.8942 Evaluate side-chains 1032 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 950 time to evaluate : 7.475 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.8452 time to fit residues: 142.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 8.9990 chunk 440 optimal weight: 0.0050 chunk 659 optimal weight: 0.0980 chunk 332 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 701 optimal weight: 8.9990 chunk 751 optimal weight: 0.9980 chunk 545 optimal weight: 10.0000 chunk 102 optimal weight: 0.0000 chunk 867 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN J 168 HIS K 7 ASN N 65 ASN O 75 ASN T 31 ASN T 56 HIS ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 HIS Y 90 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN e 5 GLN i 132 ASN ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 225 HIS m 311 ASN ** v 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 509 HIS ** v 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 83 GLN ** q 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 260 ASN q 313 ASN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 271 GLN ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 442 GLN t 453 GLN ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 124636 Z= 0.156 Angle : 0.641 21.995 177238 Z= 0.329 Chirality : 0.038 0.311 21341 Planarity : 0.005 0.184 15674 Dihedral : 20.273 179.910 38303 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.14 % Favored : 90.51 % Rotamer: Outliers : 0.92 % Allowed : 22.08 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.08), residues: 9717 helix: 0.08 (0.08), residues: 3840 sheet: -0.77 (0.14), residues: 1264 loop : -2.70 (0.08), residues: 4613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 152 HIS 0.025 0.001 HIS v 845 PHE 0.053 0.001 PHE w 53 TYR 0.028 0.001 TYR y 174 ARG 0.021 0.000 ARG S 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1049 time to evaluate : 7.614 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 outliers start: 79 outliers final: 34 residues processed: 1103 average time/residue: 1.0851 time to fit residues: 2085.7407 Evaluate side-chains 993 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 959 time to evaluate : 7.553 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.8793 time to fit residues: 66.8162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1003 optimal weight: 6.9990 chunk 1057 optimal weight: 10.0000 chunk 964 optimal weight: 20.0000 chunk 1028 optimal weight: 30.0000 chunk 1056 optimal weight: 7.9990 chunk 618 optimal weight: 20.0000 chunk 448 optimal weight: 0.3980 chunk 807 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 929 optimal weight: 0.9990 chunk 972 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 148 ASN E 121 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 GLN J 168 HIS K 167 GLN N 65 ASN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS A 114 HIS ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 509 HIS ** v 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 124636 Z= 0.211 Angle : 0.680 18.813 177238 Z= 0.346 Chirality : 0.040 0.260 21341 Planarity : 0.005 0.174 15674 Dihedral : 20.264 179.683 38303 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.24 % Favored : 89.40 % Rotamer: Outliers : 1.01 % Allowed : 22.73 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.08), residues: 9717 helix: 0.09 (0.08), residues: 3845 sheet: -0.82 (0.14), residues: 1243 loop : -2.70 (0.08), residues: 4629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP y 284 HIS 0.010 0.001 HIS w 17 PHE 0.046 0.002 PHE w 53 TYR 0.027 0.002 TYR k 316 ARG 0.014 0.001 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 965 time to evaluate : 7.698 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 outliers start: 87 outliers final: 46 residues processed: 1006 average time/residue: 1.0612 time to fit residues: 1853.3479 Evaluate side-chains 972 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 926 time to evaluate : 7.579 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.8644 time to fit residues: 85.4141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1024 optimal weight: 1.9990 chunk 675 optimal weight: 8.9990 chunk 1087 optimal weight: 5.9990 chunk 663 optimal weight: 0.0980 chunk 515 optimal weight: 10.0000 chunk 755 optimal weight: 6.9990 chunk 1140 optimal weight: 9.9990 chunk 1049 optimal weight: 30.0000 chunk 908 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 701 optimal weight: 4.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 GLN J 168 HIS K 167 GLN M 84 HIS N 65 ASN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 445 GLN ** v 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 282 GLN ** q 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 289 GLN ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 216 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.7746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 124636 Z= 0.228 Angle : 0.701 17.362 177238 Z= 0.356 Chirality : 0.041 0.257 21341 Planarity : 0.005 0.168 15674 Dihedral : 20.302 179.419 38303 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.55 % Favored : 89.10 % Rotamer: Outliers : 0.58 % Allowed : 22.85 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.08), residues: 9717 helix: 0.04 (0.08), residues: 3833 sheet: -0.78 (0.14), residues: 1235 loop : -2.73 (0.08), residues: 4649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP y 284 HIS 0.008 0.001 HIS r 228 PHE 0.064 0.002 PHE w 53 TYR 0.038 0.002 TYR u 169 ARG 0.012 0.001 ARG X 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 968 time to evaluate : 6.780 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 outliers start: 50 outliers final: 28 residues processed: 992 average time/residue: 1.0149 time to fit residues: 1746.2566 Evaluate side-chains 956 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 928 time to evaluate : 7.603 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.8259 time to fit residues: 54.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 10.0000 chunk 721 optimal weight: 1.9990 chunk 967 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 837 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 909 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 934 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 GLN J 168 HIS K 167 GLN N 65 ASN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 282 GLN ** q 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.208398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.201349 restraints weight = 202729.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.198624 restraints weight = 399981.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.195975 restraints weight = 311707.890| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 124636 Z= 0.200 Angle : 0.676 16.419 177238 Z= 0.344 Chirality : 0.040 0.259 21341 Planarity : 0.005 0.166 15674 Dihedral : 20.268 179.664 38303 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.20 % Favored : 89.46 % Rotamer: Outliers : 0.42 % Allowed : 23.29 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.08), residues: 9717 helix: 0.12 (0.08), residues: 3828 sheet: -0.83 (0.15), residues: 1210 loop : -2.68 (0.08), residues: 4679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 152 HIS 0.007 0.001 HIS v 819 PHE 0.023 0.002 PHE k 147 TYR 0.034 0.002 TYR u 169 ARG 0.012 0.000 ARG X 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32880.01 seconds wall clock time: 572 minutes 21.77 seconds (34341.77 seconds total)