Starting phenix.real_space_refine on Mon Mar 25 19:15:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unr_26630/03_2024/7unr_26630_updated.pdb" } resolution = 2.9 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= -0.001 sd= 1.011 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 Zn 2 6.06 5 P 4605 5.49 5 Mg 630 5.21 5 S 164 5.16 5 C 75121 2.51 5 N 27680 2.21 5 O 41125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 52": "OE1" <-> "OE2" Residue "b TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 175": "OE1" <-> "OE2" Residue "b TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 219": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "d TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 202": "OE1" <-> "OE2" Residue "f GLU 30": "OE1" <-> "OE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 21": "OE1" <-> "OE2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "l ASP 20": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "m ASP 82": "OD1" <-> "OD2" Residue "m ARG 117": "NH1" <-> "NH2" Residue "q ASP 18": "OD1" <-> "OD2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "t TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "L TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 49": "OD1" <-> "OD2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ASP 117": "OD1" <-> "OD2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "O TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 32": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "R GLU 72": "OE1" <-> "OE2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U ASP 65": "OD1" <-> "OD2" Residue "V PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 5": "OE1" <-> "OE2" Residue "2 GLU 42": "OE1" <-> "OE2" Residue "4 ASP 45": "OD1" <-> "OD2" Residue "4 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 20": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149327 Number of models: 1 Model: "" Number of chains: 82 Chain: "a" Number of atoms: 32675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 32675 Classifications: {'RNA': 1522} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 123, 'rna2p_pyr': 87, 'rna3p': 8, 'rna3p_pur': 742, 'rna3p_pyr': 561} Link IDs: {'rna2p': 211, 'rna3p': 1310} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1751 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "e" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1134 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 857 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 104} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "g" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1187 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 793 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "k" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 879 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "m" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 892 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "n" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 800 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "q" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 480 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 671 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 506 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "v" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 65} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3500 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 467} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 61891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2884, 61891 Classifications: {'RNA': 2884} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna2p_pur': 275, 'rna2p_pyr': 168, 'rna3p': 8, 'rna3p_pur': 1369, 'rna3p_pyr': 1059} Link IDs: {'rna2p': 448, 'rna3p': 2435} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 103} Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2072 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "D" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1588 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "E" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1521 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1407 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 168} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1323 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 964 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 668 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 718 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1130 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 132} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1066 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "O" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1085 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "P" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "Q" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "S" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "T" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "W" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1445 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "Y" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "Z" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "3" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 440 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "5" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "8" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Unusual residues: {' MG': 136} Classifications: {'undetermined': 136} Link IDs: {None: 135} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 471 Unusual residues: {' MG': 471} Classifications: {'undetermined': 471} Link IDs: {None: 470} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0ZMS SG CYS 3 16 125.493 232.705 108.753 1.00 76.66 S ATOM A0ZN4 SG CYS 3 18 122.893 235.364 107.794 1.00 77.65 S ATOM A0ZR0 SG CYS 3 37 122.105 233.063 110.568 1.00 76.10 S ATOM A0ZRL SG CYS 3 40 122.432 231.618 107.012 1.00 78.36 S ATOM A117V SG CYS 8 11 58.321 143.311 133.707 1.00 44.89 S ATOM A118K SG CYS 8 14 59.649 142.316 137.095 1.00 43.57 S ATOM A11BI SG CYS 8 27 57.952 139.754 134.861 1.00 46.98 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU e 152 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU e 152 " occ=0.00 residue: pdb=" N VAL e 154 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL e 154 " occ=0.00 residue: pdb=" N ALA e 155 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 155 " occ=0.00 residue: pdb=" N ALA e 156 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 156 " occ=0.00 residue: pdb=" N LYS e 157 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS e 157 " occ=0.00 residue: pdb=" N ARG e 158 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG e 158 " occ=0.00 residue: pdb=" N GLY e 159 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY e 159 " occ=0.00 residue: pdb=" N FME v 103 " occ=0.80 ... (8 atoms not shown) pdb=" O1 FME v 103 " occ=0.80 Time building chain proxies: 57.23, per 1000 atoms: 0.38 Number of scatterers: 149327 At special positions: 0 Unit cell: (247.35, 254.15, 274.55, 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) Zn 2 29.99 S 164 16.00 P 4605 15.00 Mg 630 11.99 O 41125 8.00 N 27680 7.00 C 75121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.46 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 18 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 37 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " Number of angles added : 9 12786 Ramachandran restraints generated. 6393 Oldfield, 0 Emsley, 6393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11866 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: 189 helices and 86 sheets defined 37.6% alpha, 20.7% beta 1522 base pairs and 2332 stacking pairs defined. Time for finding SS restraints: 80.44 Creating SS restraints... Processing helix chain 'b' and resid 6 through 13 removed outlier: 3.703A pdb=" N LEU b 10 " --> pdb=" O MET b 6 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.118A pdb=" N GLY b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE b 32 " --> pdb=" O GLY b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.637A pdb=" N THR b 46 " --> pdb=" O ASN b 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU b 47 " --> pdb=" O LEU b 43 " (cutoff:3.500A) Proline residue: b 48 - end of helix removed outlier: 5.235A pdb=" N GLY b 63 " --> pdb=" O ARG b 59 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 86 removed outlier: 6.778A pdb=" N LYS b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE b 79 " --> pdb=" O SER b 75 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG b 86 " --> pdb=" O GLU b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 125 removed outlier: 3.984A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 4.103A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.887A pdb=" N GLY b 227 " --> pdb=" O ARG b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.883A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.590A pdb=" N LEU c 47 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS c 48 " --> pdb=" O GLN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.643A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 95 Processing helix chain 'c' and resid 112 through 127 removed outlier: 3.621A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.651A pdb=" N VAL c 138 " --> pdb=" O MET c 134 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.658A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 4.893A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 3.894A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 removed outlier: 3.975A pdb=" N GLY d 106 " --> pdb=" O VAL d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.786A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 5.158A pdb=" N ASN d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.732A pdb=" N ALA d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY d 166 " --> pdb=" O CYS d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.961A pdb=" N LEU d 191 " --> pdb=" O ALA d 187 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.727A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 4.595A pdb=" N ASN e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 133 through 148 removed outlier: 4.249A pdb=" N ASN e 147 " --> pdb=" O LYS e 143 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 156 removed outlier: 3.579A pdb=" N VAL e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA e 155 " --> pdb=" O PRO e 151 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA e 156 " --> pdb=" O GLU e 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 150 through 156' Processing helix chain 'e' and resid 159 through 164 removed outlier: 4.453A pdb=" N GLU e 163 " --> pdb=" O GLY e 159 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 164' Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.150A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.539A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.593A pdb=" N GLY g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.559A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.656A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.585A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.646A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.160A pdb=" N GLY i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 56 Proline residue: i 51 - end of helix removed outlier: 4.126A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.613A pdb=" N LEU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.994A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 88 removed outlier: 4.193A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.692A pdb=" N SER k 50 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY k 51 " --> pdb=" O SER k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.135A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 4.679A pdb=" N GLU k 76 " --> pdb=" O GLN k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.688A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN k 101 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.584A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.087A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.924A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY m 38 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.765A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.298A pdb=" N GLN m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS m 62 " --> pdb=" O ASN m 58 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.037A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.550A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.599A pdb=" N LYS n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 removed outlier: 3.513A pdb=" N GLU n 26 " --> pdb=" O LYS n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 4.139A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN n 51 " --> pdb=" O ALA n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.882A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.731A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE o 43 " --> pdb=" O LEU o 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.798A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 81 removed outlier: 3.507A pdb=" N ALA p 81 " --> pdb=" O ASP p 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.791A pdb=" N ALA r 31 " --> pdb=" O ASN r 27 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.587A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.594A pdb=" N LEU r 65 " --> pdb=" O ARG r 61 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 24 removed outlier: 5.199A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.427A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA s 76 " --> pdb=" O GLY s 72 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 removed outlier: 4.289A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 88 removed outlier: 3.908A pdb=" N THR t 88 " --> pdb=" O LYS t 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.732A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU u 16 " --> pdb=" O PHE u 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.515A pdb=" N ARG u 35 " --> pdb=" O GLU u 31 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 63 removed outlier: 4.445A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) Processing helix chain 'x' and resid 354 through 367 removed outlier: 3.505A pdb=" N ILE x 362 " --> pdb=" O LEU x 358 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG x 363 " --> pdb=" O LEU x 359 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL x 367 " --> pdb=" O ARG x 363 " (cutoff:3.500A) Processing helix chain 'x' and resid 398 through 409 removed outlier: 5.791A pdb=" N PHE x 402 " --> pdb=" O GLY x 398 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N THR x 403 " --> pdb=" O HIS x 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET x 405 " --> pdb=" O ALA x 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG x 406 " --> pdb=" O PHE x 402 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG x 408 " --> pdb=" O ALA x 404 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY x 409 " --> pdb=" O MET x 405 " (cutoff:3.500A) Processing helix chain 'x' and resid 427 through 441 removed outlier: 4.021A pdb=" N GLU x 432 " --> pdb=" O PRO x 428 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA x 440 " --> pdb=" O HIS x 436 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY x 441 " --> pdb=" O ALA x 437 " (cutoff:3.500A) Processing helix chain 'x' and resid 457 through 469 removed outlier: 4.665A pdb=" N ILE x 461 " --> pdb=" O ASN x 457 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA x 467 " --> pdb=" O ASN x 463 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU x 468 " --> pdb=" O GLY x 464 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP x 469 " --> pdb=" O LEU x 465 " (cutoff:3.500A) Processing helix chain 'x' and resid 491 through 507 removed outlier: 3.626A pdb=" N VAL x 505 " --> pdb=" O LEU x 501 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU x 506 " --> pdb=" O GLN x 502 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU x 507 " --> pdb=" O ALA x 503 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 623 removed outlier: 3.814A pdb=" N LYS x 616 " --> pdb=" O PHE x 612 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA x 618 " --> pdb=" O GLU x 614 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS x 621 " --> pdb=" O LEU x 617 " (cutoff:3.500A) Processing helix chain 'x' and resid 624 through 629 removed outlier: 5.232A pdb=" N PHE x 629 " --> pdb=" O LEU x 625 " (cutoff:3.500A) Processing helix chain 'x' and resid 648 through 661 removed outlier: 4.372A pdb=" N GLY x 661 " --> pdb=" O GLY x 657 " (cutoff:3.500A) Processing helix chain 'x' and resid 680 through 691 Processing helix chain 'x' and resid 702 through 713 Processing helix chain 'x' and resid 721 through 735 removed outlier: 4.186A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 removed outlier: 3.585A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 17' Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.019A pdb=" N LEU C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.765A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.943A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.307A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 261 through 269 removed outlier: 6.503A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 269' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.378A pdb=" N SER C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.601A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.157A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.651A pdb=" N VAL E 27 " --> pdb=" O ASN E 23 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.373A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 removed outlier: 3.556A pdb=" N GLU E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 4.185A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.506A pdb=" N ALA E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.637A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 4.054A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 21 removed outlier: 3.785A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 removed outlier: 5.327A pdb=" N GLU F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.784A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.318A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.555A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.804A pdb=" N LYS G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix No H-bonds generated for 'chain 'G' and resid 2 through 8' Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.833A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.036A pdb=" N PHE G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 51 removed outlier: 3.705A pdb=" N ALA H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 72 removed outlier: 3.991A pdb=" N LYS H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.636A pdb=" N ALA H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 22 removed outlier: 4.150A pdb=" N ILE I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL I 12 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 49 Processing helix chain 'I' and resid 56 through 64 removed outlier: 3.824A pdb=" N LYS I 61 " --> pdb=" O ASN I 57 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 103 removed outlier: 6.415A pdb=" N ARG I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.997A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN J 43 " --> pdb=" O CYS J 39 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR J 46 " --> pdb=" O PHE J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 85 removed outlier: 3.695A pdb=" N LEU J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY J 85 " --> pdb=" O LYS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 114 removed outlier: 3.552A pdb=" N LEU J 106 " --> pdb=" O THR J 102 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 4.359A pdb=" N ARG J 127 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER J 132 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.525A pdb=" N THR L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.180A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.528A pdb=" N ARG L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS L 121 " --> pdb=" O ASP L 117 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 4.097A pdb=" N ARG M 107 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 108' Processing helix chain 'M' and resid 111 through 118 removed outlier: 3.551A pdb=" N VAL M 115 " --> pdb=" O PHE M 111 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU M 117 " --> pdb=" O LYS M 113 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA M 118 " --> pdb=" O ILE M 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 Processing helix chain 'N' and resid 68 through 73 removed outlier: 4.561A pdb=" N MET N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 68 through 73' Processing helix chain 'N' and resid 78 through 83 removed outlier: 3.930A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA N 83 " --> pdb=" O THR N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 83' Processing helix chain 'N' and resid 91 through 99 removed outlier: 4.364A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 3.687A pdb=" N ALA N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 6.090A pdb=" N ILE O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA O 53 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.555A pdb=" N ALA O 123 " --> pdb=" O ALA O 119 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.526A pdb=" N GLN P 22 " --> pdb=" O LYS P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 57 removed outlier: 3.716A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 3.732A pdb=" N LYS P 56 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 Processing helix chain 'P' and resid 72 through 88 removed outlier: 4.221A pdb=" N PHE P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN P 81 " --> pdb=" O GLY P 77 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS P 85 " --> pdb=" O ASN P 81 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 23 removed outlier: 3.688A pdb=" N ARG Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG Q 20 " --> pdb=" O ARG Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 85 removed outlier: 3.997A pdb=" N LYS Q 72 " --> pdb=" O ASP Q 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA Q 78 " --> pdb=" O GLY Q 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 113 Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.857A pdb=" N GLN R 7 " --> pdb=" O ASN R 3 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN R 8 " --> pdb=" O LYS R 4 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU R 12 " --> pdb=" O GLN R 8 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 105 removed outlier: 5.002A pdb=" N ARG R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 105' Processing helix chain 'S' and resid 6 through 22 removed outlier: 3.601A pdb=" N LYS S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.066A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.751A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.225A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 Processing helix chain 'S' and resid 102 through 117 removed outlier: 3.637A pdb=" N SER S 116 " --> pdb=" O LYS S 112 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 25 removed outlier: 4.001A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.550A pdb=" N LEU U 33 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER U 39 " --> pdb=" O LEU U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 4.146A pdb=" N GLU U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL U 50 " --> pdb=" O ILE U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.962A pdb=" N LEU U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 2 through 10 removed outlier: 3.552A pdb=" N VAL V 6 " --> pdb=" O ASN V 2 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE V 7 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS V 8 " --> pdb=" O GLU V 4 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 2 through 10' Processing helix chain 'V' and resid 16 through 26 removed outlier: 3.642A pdb=" N ASP V 24 " --> pdb=" O THR V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 50 removed outlier: 3.540A pdb=" N GLU V 47 " --> pdb=" O LYS V 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 25 removed outlier: 3.688A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 56 removed outlier: 3.727A pdb=" N LYS X 52 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 122 Processing helix chain 'X' and resid 161 through 166 removed outlier: 3.808A pdb=" N LEU X 165 " --> pdb=" O HIS X 161 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS X 166 " --> pdb=" O LEU X 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 161 through 166' Processing helix chain 'X' and resid 173 through 179 removed outlier: 5.163A pdb=" N ALA X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY X 179 " --> pdb=" O GLN X 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 63 removed outlier: 3.518A pdb=" N ARG Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 75 removed outlier: 3.505A pdb=" N GLY Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 9 removed outlier: 4.069A pdb=" N GLU 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 35 removed outlier: 3.997A pdb=" N GLU 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN 1 17 " --> pdb=" O GLN 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 61 removed outlier: 4.578A pdb=" N SER 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG 1 48 " --> pdb=" O SER 1 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN 1 59 " --> pdb=" O THR 1 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN 1 60 " --> pdb=" O VAL 1 56 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.597A pdb=" N LEU 2 26 " --> pdb=" O CYS 2 22 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.699A pdb=" N MET 2 46 " --> pdb=" O GLU 2 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA 2 50 " --> pdb=" O MET 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 Processing helix chain '4' and resid 9 through 19 removed outlier: 3.756A pdb=" N ARG 4 16 " --> pdb=" O ALA 4 12 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 removed outlier: 3.879A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.787A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 removed outlier: 3.654A pdb=" N VAL 6 30 " --> pdb=" O ASN 6 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS 6 37 " --> pdb=" O ARG 6 33 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.525A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 36 removed outlier: 4.675A pdb=" N MET 7 35 " --> pdb=" O ILE 7 31 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR 7 36 " --> pdb=" O LEU 7 32 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 31 through 36' Processing helix chain '7' and resid 37 through 45 removed outlier: 3.986A pdb=" N ARG 7 44 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY 7 45 " --> pdb=" O ARG 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 62 removed outlier: 4.915A pdb=" N ALA 7 55 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG 7 56 " --> pdb=" O SER 7 52 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.502A pdb=" N VAL b 186 " --> pdb=" O VAL b 163 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.696A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.628A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 140 through 144 removed outlier: 4.423A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE d 182 " --> pdb=" O ASP d 141 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP d 174 " --> pdb=" O ALA d 179 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 13 through 17 removed outlier: 6.607A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 85 through 89 removed outlier: 3.952A pdb=" N GLN e 98 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU e 125 " --> pdb=" O GLN e 98 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 34 through 41 Processing sheet with id= 8, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.510A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS f 56 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 44 through 47 removed outlier: 3.530A pdb=" N ALA f 57 " --> pdb=" O ARG f 45 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.950A pdb=" N LEU g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.256A pdb=" N THR h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN h 58 " --> pdb=" O SER h 52 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP h 48 " --> pdb=" O GLU h 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.740A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE h 103 " --> pdb=" O LEU h 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 14, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.164A pdb=" N ALA j 61 " --> pdb=" O ILE j 53 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 29 through 36 removed outlier: 3.896A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.424A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.548A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 4 through 11 removed outlier: 4.032A pdb=" N GLY p 37 " --> pdb=" O LEU p 19 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 10 through 14 Processing sheet with id= 20, first strand: chain 'q' and resid 22 through 34 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 30 through 34 removed outlier: 4.523A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL s 62 " --> pdb=" O LEU s 47 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'x' and resid 380 through 385 removed outlier: 5.537A pdb=" N GLY x 380 " --> pdb=" O ASP x 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP x 395 " --> pdb=" O GLY x 380 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL x 347 " --> pdb=" O LEU x 394 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL x 420 " --> pdb=" O ALA x 447 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL x 446 " --> pdb=" O PRO x 480 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'x' and resid 522 through 526 removed outlier: 4.470A pdb=" N GLU x 522 " --> pdb=" O THR x 534 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR x 534 " --> pdb=" O VAL x 521 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG x 517 " --> pdb=" O GLN x 538 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY x 516 " --> pdb=" O VAL x 594 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP x 590 " --> pdb=" O VAL x 520 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET x 547 " --> pdb=" O VAL x 595 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'x' and resid 667 through 672 removed outlier: 5.924A pdb=" N GLN x 668 " --> pdb=" O LYS x 638 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU x 644 " --> pdb=" O VAL x 672 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY x 673 " --> pdb=" O ILE x 642 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU x 644 " --> pdb=" O GLY x 673 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY x 677 " --> pdb=" O ALA x 646 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'x' and resid 715 through 718 Processing sheet with id= 26, first strand: chain 'x' and resid 742 through 745 removed outlier: 3.993A pdb=" N ARG x 742 " --> pdb=" O VAL x 834 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP x 826 " --> pdb=" O VAL x 751 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL x 751 " --> pdb=" O ASP x 826 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY x 747 " --> pdb=" O VAL x 830 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY x 765 " --> pdb=" O ARG x 752 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG x 797 " --> pdb=" O GLY x 813 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'x' and resid 788 through 791 removed outlier: 3.709A pdb=" N VAL x 781 " --> pdb=" O PHE x 789 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'x' and resid 338 through 341 removed outlier: 4.106A pdb=" N ARG x 341 " --> pdb=" O LEU x 508 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N LEU x 508 " --> pdb=" O ARG x 341 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'x' and resid 533 through 536 removed outlier: 3.703A pdb=" N ALA x 533 " --> pdb=" O ILE x 579 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'x' and resid 641 through 645 Processing sheet with id= 31, first strand: chain 'x' and resid 779 through 782 Processing sheet with id= 32, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.687A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 116 through 119 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.374A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ALA C 170 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.522A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.224A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 199 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP D 200 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 37 through 41 removed outlier: 4.355A pdb=" N GLU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR D 46 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP D 94 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.638A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 25 through 30 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'D' and resid 48 through 52 Processing sheet with id= 41, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.391A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 1 through 5 removed outlier: 6.177A pdb=" N LEU E 3 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 11 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 5 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 41 through 46 removed outlier: 7.529A pdb=" N GLY E 41 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 90 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA E 86 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.755A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.336A pdb=" N ILE F 85 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 89 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 15 through 19 Processing sheet with id= 47, first strand: chain 'G' and resid 42 through 45 removed outlier: 4.105A pdb=" N ARG G 51 " --> pdb=" O GLN G 45 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.108A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 50, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.074A pdb=" N GLU H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'H' and resid 76 through 82 removed outlier: 4.447A pdb=" N VAL H 77 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA H 81 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 141 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE H 127 " --> pdb=" O LEU H 143 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'I' and resid 23 through 29 removed outlier: 3.568A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 9 through 14 removed outlier: 3.870A pdb=" N ILE J 9 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU J 11 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE J 58 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 68 " --> pdb=" O THR J 60 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.880A pdb=" N ASP L 19 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.558A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.220A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU M 86 " --> pdb=" O ALA M 11 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR M 59 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP M 37 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 68 through 71 removed outlier: 4.311A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 63 through 66 removed outlier: 4.299A pdb=" N LYS M 66 " --> pdb=" O GLY M 81 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY M 81 " --> pdb=" O LYS M 66 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 74 through 77 Processing sheet with id= 60, first strand: chain 'O' and resid 38 through 41 removed outlier: 3.745A pdb=" N TYR O 92 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.720A pdb=" N TYR O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'O' and resid 31 through 37 removed outlier: 8.335A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG O 134 " --> pdb=" O GLU O 31 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA O 128 " --> pdb=" O THR O 37 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'P' and resid 33 through 37 removed outlier: 5.780A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 50 through 53 removed outlier: 4.026A pdb=" N ALA Q 50 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'R' and resid 39 through 46 removed outlier: 6.414A pdb=" N THR R 26 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER R 84 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'R' and resid 50 through 53 removed outlier: 3.601A pdb=" N ALA R 50 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER R 58 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 11 through 15 removed outlier: 4.027A pdb=" N LEU T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'T' and resid 18 through 23 removed outlier: 4.123A pdb=" N GLU T 18 " --> pdb=" O ILE T 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU T 95 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR T 60 " --> pdb=" O THR T 99 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU T 31 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'T' and resid 65 through 68 Processing sheet with id= 70, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.203A pdb=" N HIS T 83 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'U' and resid 2 through 8 removed outlier: 4.686A pdb=" N SER U 100 " --> pdb=" O GLY U 79 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'V' and resid 28 through 32 removed outlier: 5.328A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP V 78 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS V 63 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL V 57 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'W' and resid 9 through 13 removed outlier: 6.596A pdb=" N GLU W 9 " --> pdb=" O PHE W 72 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN W 68 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.609A pdb=" N ASN W 39 " --> pdb=" O ALA W 62 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS W 60 " --> pdb=" O ILE W 41 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'W' and resid 81 through 87 removed outlier: 7.649A pdb=" N ARG W 81 " --> pdb=" O LYS W 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE W 92 " --> pdb=" O LYS W 85 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU W 87 " --> pdb=" O LYS W 90 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS W 90 " --> pdb=" O GLU W 87 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG W 93 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS W 100 " --> pdb=" O PHE W 95 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'X' and resid 72 through 75 removed outlier: 3.569A pdb=" N LEU X 6 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER X 42 " --> pdb=" O ARG X 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA X 92 " --> pdb=" O PRO X 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS X 91 " --> pdb=" O GLN X 81 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA X 79 " --> pdb=" O ASP X 93 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'X' and resid 125 through 130 No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'X' and resid 132 through 138 removed outlier: 6.854A pdb=" N SER X 132 " --> pdb=" O LEU X 109 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Y' and resid 29 through 32 removed outlier: 5.092A pdb=" N GLN Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY Y 65 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER Y 81 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Y' and resid 37 through 40 removed outlier: 3.507A pdb=" N VAL Y 38 " --> pdb=" O LEU Y 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN Y 40 " --> pdb=" O HIS Y 57 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS Y 57 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.517A pdb=" N ARG Z 27 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG Z 45 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '2' and resid 32 through 38 removed outlier: 4.241A pdb=" N HIS 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL 2 6 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 2 37 " --> pdb=" O VAL 2 4 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS 2 5 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '3' and resid 12 through 16 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain '5' and resid 16 through 22 removed outlier: 3.671A pdb=" N THR 5 19 " --> pdb=" O ILE 5 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE 5 44 " --> pdb=" O SER 5 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '7' and resid 21 through 24 removed outlier: 6.391A pdb=" N LEU 7 21 " --> pdb=" O LEU 7 49 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain '8' and resid 23 through 27 removed outlier: 4.410A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) 1969 hydrogen bonds defined for protein. 5823 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3847 hydrogen bonds 6030 hydrogen bond angles 0 basepair planarities 1522 basepair parallelities 2332 stacking parallelities Total time for adding SS restraints: 381.44 Time building geometry restraints manager: 62.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18906 1.33 - 1.45: 70468 1.45 - 1.58: 62130 1.58 - 1.70: 9196 1.70 - 1.83: 287 Bond restraints: 160987 Sorted by residual: bond pdb=" C4 5MU A1926 " pdb=" C5 5MU A1926 " ideal model delta sigma weight residual 1.802 1.477 0.325 2.00e-02 2.50e+03 2.65e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" N1 5MU A1926 " pdb=" C6 5MU A1926 " ideal model delta sigma weight residual 1.635 1.333 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.24e+02 bond pdb=" C5 5MU A1926 " pdb=" C6 5MU A1926 " ideal model delta sigma weight residual 1.155 1.385 -0.230 2.00e-02 2.50e+03 1.33e+02 ... (remaining 160982 not shown) Histogram of bond angle deviations from ideal: 74.01 - 87.03: 3 87.03 - 100.04: 39 100.04 - 113.06: 118920 113.06 - 126.07: 105717 126.07 - 139.09: 15560 Bond angle restraints: 240239 Sorted by residual: angle pdb=" O3' C v 75 " pdb=" P A v 76 " pdb=" OP1 A v 76 " ideal model delta sigma weight residual 108.00 74.01 33.99 3.00e+00 1.11e-01 1.28e+02 angle pdb=" CA PRO D 152 " pdb=" N PRO D 152 " pdb=" CD PRO D 152 " ideal model delta sigma weight residual 112.00 96.38 15.62 1.40e+00 5.10e-01 1.25e+02 angle pdb=" C PRO D 152 " pdb=" CA PRO D 152 " pdb=" CB PRO D 152 " ideal model delta sigma weight residual 111.56 127.42 -15.86 1.65e+00 3.67e-01 9.24e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP1 U A1095 " ideal model delta sigma weight residual 108.00 80.82 27.18 3.00e+00 1.11e-01 8.21e+01 angle pdb=" O3' C v 75 " pdb=" P A v 76 " pdb=" OP2 A v 76 " ideal model delta sigma weight residual 108.00 134.27 -26.27 3.00e+00 1.11e-01 7.67e+01 ... (remaining 240234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 91314 35.86 - 71.71: 10159 71.71 - 107.57: 1180 107.57 - 143.43: 24 143.43 - 179.29: 38 Dihedral angle restraints: 102715 sinusoidal: 84265 harmonic: 18450 Sorted by residual: dihedral pdb=" O4' U A1913 " pdb=" C1' U A1913 " pdb=" N1 U A1913 " pdb=" C2 U A1913 " ideal model delta sinusoidal sigma weight residual 200.00 23.48 176.52 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 836 " pdb=" C1' U A 836 " pdb=" N1 U A 836 " pdb=" C2 U A 836 " ideal model delta sinusoidal sigma weight residual -160.00 10.33 -170.33 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U a 359 " pdb=" C1' U a 359 " pdb=" N1 U a 359 " pdb=" C2 U a 359 " ideal model delta sinusoidal sigma weight residual 200.00 37.11 162.89 1 1.50e+01 4.44e-03 8.34e+01 ... (remaining 102712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.391: 30600 0.391 - 0.783: 3 0.783 - 1.174: 0 1.174 - 1.566: 0 1.566 - 1.957: 1 Chirality restraints: 30604 Sorted by residual: chirality pdb=" P U A1095 " pdb=" OP1 U A1095 " pdb=" OP2 U A1095 " pdb=" O5' U A1095 " both_signs ideal model delta sigma weight residual True 2.41 0.45 1.96 2.00e-01 2.50e+01 9.58e+01 chirality pdb=" CA PRO D 152 " pdb=" N PRO D 152 " pdb=" C PRO D 152 " pdb=" CB PRO D 152 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C3' U A1016 " pdb=" C4' U A1016 " pdb=" O3' U A1016 " pdb=" C2' U A1016 " both_signs ideal model delta sigma weight residual False -2.48 -1.91 -0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 30601 not shown) Planarity restraints: 13402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2056 " 0.077 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' 7MG A2056 " 0.426 2.00e-02 2.50e+03 pdb=" O4' 7MG A2056 " 0.541 2.00e-02 2.50e+03 pdb=" C3' 7MG A2056 " -0.598 2.00e-02 2.50e+03 pdb=" O3' 7MG A2056 " -0.656 2.00e-02 2.50e+03 pdb=" C2' 7MG A2056 " -0.156 2.00e-02 2.50e+03 pdb=" O2' 7MG A2056 " 1.012 2.00e-02 2.50e+03 pdb=" C1' 7MG A2056 " 0.230 2.00e-02 2.50e+03 pdb=" N9 7MG A2056 " -0.876 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2485 " -0.058 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' OMC A2485 " -0.439 2.00e-02 2.50e+03 pdb=" O4' OMC A2485 " -0.604 2.00e-02 2.50e+03 pdb=" C3' OMC A2485 " 0.592 2.00e-02 2.50e+03 pdb=" O3' OMC A2485 " 0.632 2.00e-02 2.50e+03 pdb=" C2' OMC A2485 " 0.180 2.00e-02 2.50e+03 pdb=" O2' OMC A2485 " -0.973 2.00e-02 2.50e+03 pdb=" C1' OMC A2485 " -0.223 2.00e-02 2.50e+03 pdb=" N1 OMC A2485 " 0.892 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1510 " 0.055 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' 2MG a1510 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG a1510 " 0.611 2.00e-02 2.50e+03 pdb=" C3' 2MG a1510 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG a1510 " -0.623 2.00e-02 2.50e+03 pdb=" C2' 2MG a1510 " -0.180 2.00e-02 2.50e+03 pdb=" O2' 2MG a1510 " 0.965 2.00e-02 2.50e+03 pdb=" C1' 2MG a1510 " 0.228 2.00e-02 2.50e+03 pdb=" N9 2MG a1510 " -0.901 2.00e-02 2.50e+03 ... (remaining 13399 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 1074 2.48 - 3.09: 92416 3.09 - 3.69: 261893 3.69 - 4.30: 411012 4.30 - 4.90: 564476 Nonbonded interactions: 1330871 Sorted by model distance: nonbonded pdb=" OP1 A A2020 " pdb="MG MG A3415 " model vdw 1.879 2.170 nonbonded pdb=" N7 G a 794 " pdb="MG MG a3119 " model vdw 1.894 2.250 nonbonded pdb=" N7 G A1989 " pdb="MG MG A3438 " model vdw 1.895 2.250 nonbonded pdb=" N7 G A 551 " pdb="MG MG A3458 " model vdw 1.895 2.250 nonbonded pdb=" N1 A A2601 " pdb="MG MG A3418 " model vdw 1.895 2.250 ... (remaining 1330866 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 30.880 Check model and map are aligned: 1.660 Set scattering table: 1.000 Process input model: 709.010 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 768.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.325 160987 Z= 0.340 Angle : 0.644 33.988 240239 Z= 0.331 Chirality : 0.040 1.957 30604 Planarity : 0.019 0.590 13402 Dihedral : 22.699 179.287 90849 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.18 % Favored : 92.43 % Rotamer: Outliers : 0.26 % Allowed : 0.50 % Favored : 99.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % 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: -1.63 (0.10), residues: 6393 helix: -0.23 (0.12), residues: 1908 sheet: -0.64 (0.14), residues: 1315 loop : -1.81 (0.10), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP b 23 HIS 0.009 0.001 HIS P 16 PHE 0.032 0.002 PHE e 142 TYR 0.025 0.002 TYR e 12 ARG 0.016 0.000 ARG x 613 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12786 Ramachandran restraints generated. 6393 Oldfield, 0 Emsley, 6393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12786 Ramachandran restraints generated. 6393 Oldfield, 0 Emsley, 6393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 5269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1237 time to evaluate : 6.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 91 TYR cc_start: 0.8965 (p90) cc_final: 0.8757 (p90) REVERT: b 142 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7368 (tm-30) REVERT: g 113 GLU cc_start: 0.7695 (pt0) cc_final: 0.7422 (pp20) REVERT: q 9 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6486 (mtm-85) REVERT: r 45 THR cc_start: 0.8978 (p) cc_final: 0.8755 (p) REVERT: O 31 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7238 (tp30) outliers start: 13 outliers final: 11 residues processed: 1248 average time/residue: 2.2465 time to fit residues: 3996.4545 Evaluate side-chains 1010 residues out of total 5269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 998 time to evaluate : 6.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 116 ILE Chi-restraints excluded: chain q residue 9 ARG Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain x residue 355 LYS Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain Z residue 2 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 917 optimal weight: 6.9990 chunk 823 optimal weight: 5.9990 chunk 456 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 555 optimal weight: 8.9990 chunk 439 optimal weight: 10.0000 chunk 851 optimal weight: 20.0000 chunk 329 optimal weight: 7.9990 chunk 517 optimal weight: 8.9990 chunk 633 optimal weight: 6.9990 chunk 986 optimal weight: 0.0980 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 15 HIS c 18 HIS c 123 GLN c 190 HIS e 20 ASN e 71 ASN e 83 GLN e 147 ASN e 149 GLN g 21 GLN h 18 GLN h 58 GLN k 72 GLN k 85 ASN l 5 ASN l 6 GLN l 59 ASN m 14 HIS m 76 ASN n 14 GLN n 49 GLN o 37 ASN o 40 GLN o 46 ASN o 61 ASN ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN t 68 HIS u 9 ASN ** x 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 641 ASN C 21 ASN C 252 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 155 ASN F 127 ASN G 128 GLN G 143 GLN H 20 ASN L 23 GLN M 3 GLN N 55 GLN N 93 GLN N 104 HIS P 9 HIS ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 GLN R 15 ASN R 76 GLN S 71 GLN S 72 ASN V 77 ASN W 103 GLN Y 29 GLN Z 23 ASN ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN 2 13 ASN 2 18 ASN 6 26 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 160987 Z= 0.344 Angle : 0.715 27.366 240239 Z= 0.380 Chirality : 0.043 1.951 30604 Planarity : 0.007 0.169 13402 Dihedral : 23.151 179.375 78896 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.10 % Favored : 91.48 % Rotamer: Outliers : 3.02 % Allowed : 15.24 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.03 % 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: -1.42 (0.10), residues: 6393 helix: 0.13 (0.12), residues: 1997 sheet: -0.47 (0.14), residues: 1283 loop : -1.89 (0.10), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 23 HIS 0.010 0.001 HIS N 17 PHE 0.039 0.002 PHE F 114 TYR 0.022 0.002 TYR b 213 ARG 0.009 0.001 ARG x 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12786 Ramachandran restraints generated. 6393 Oldfield, 0 Emsley, 6393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12786 Ramachandran restraints generated. 6393 Oldfield, 0 Emsley, 6393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1044 time to evaluate : 6.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 91 TYR cc_start: 0.9036 (p90) cc_final: 0.8787 (p90) REVERT: d 73 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7617 (mtp85) REVERT: f 31 GLU cc_start: 0.7562 (mp0) cc_final: 0.7099 (tp30) REVERT: f 79 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7905 (ttt90) REVERT: g 142 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7119 (m90) REVERT: h 114 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7628 (ptt90) REVERT: i 49 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7710 (mtm110) REVERT: j 37 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7210 (mtt90) REVERT: u 21 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6343 (mpt90) REVERT: x 536 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7913 (tp) REVERT: D 181 ASP cc_start: 0.7660 (t0) cc_final: 0.7338 (t0) REVERT: D 183 GLU cc_start: 0.7296 (pm20) cc_final: 0.7088 (pm20) REVERT: E 172 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: F 123 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7261 (p0) REVERT: N 111 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7581 (ptp) REVERT: N 132 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6729 (mtp85) REVERT: O 31 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7449 (tp30) REVERT: P 33 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8107 (tp) REVERT: Q 75 GLN cc_start: 0.8581 (pp30) cc_final: 0.8334 (pp30) REVERT: Q 79 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7483 (mt-10) REVERT: R 90 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7081 (mmt90) REVERT: R 112 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7694 (ttmm) REVERT: U 1 MET cc_start: 0.7713 (tpt) cc_final: 0.7425 (tpt) REVERT: W 99 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: X 133 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: 4 23 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6244 (mt-10) outliers start: 152 outliers final: 87 residues processed: 1107 average time/residue: 2.2065 time to fit residues: 3543.8538 Evaluate side-chains 1091 residues out of total 5269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 991 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 75 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 114 ARG Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 90 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 116 ILE Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain x residue 355 LYS Chi-restraints excluded: chain x residue 378 HIS Chi-restraints excluded: chain x residue 390 MET Chi-restraints excluded: chain x residue 492 VAL Chi-restraints excluded: chain x residue 536 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 642 ILE Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 763 ILE Chi-restraints excluded: chain x residue 816 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 48 LYS Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 99 GLN Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain 4 residue 23 GLU Chi-restraints excluded: chain 5 residue 47 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.6084 > 50: distance: 52 - 128: 21.420 distance: 55 - 125: 12.198 distance: 112 - 117: 11.609 distance: 117 - 118: 22.665 distance: 118 - 119: 30.866 distance: 118 - 121: 21.571 distance: 119 - 120: 38.661 distance: 119 - 125: 12.054 distance: 120 - 247: 33.373 distance: 121 - 122: 28.429 distance: 122 - 123: 13.566 distance: 122 - 124: 29.157 distance: 125 - 126: 19.274 distance: 126 - 127: 21.646 distance: 126 - 129: 23.204 distance: 127 - 128: 38.582 distance: 127 - 133: 13.473 distance: 129 - 130: 12.070 distance: 129 - 131: 29.354 distance: 130 - 132: 24.177 distance: 133 - 134: 25.790 distance: 133 - 235: 33.816 distance: 134 - 135: 29.213 distance: 134 - 137: 17.153 distance: 135 - 136: 21.576 distance: 135 - 144: 30.117 distance: 136 - 232: 10.104 distance: 137 - 138: 23.352 distance: 138 - 139: 19.823 distance: 139 - 140: 12.559 distance: 140 - 141: 5.505 distance: 141 - 142: 6.256 distance: 141 - 143: 6.520 distance: 144 - 145: 32.912 distance: 145 - 146: 46.986 distance: 146 - 147: 19.921 distance: 146 - 148: 38.110 distance: 148 - 149: 13.609 distance: 149 - 150: 57.985 distance: 150 - 151: 41.399 distance: 152 - 153: 17.138 distance: 153 - 154: 40.126 distance: 153 - 156: 40.496 distance: 154 - 155: 34.686 distance: 154 - 163: 34.417 distance: 156 - 157: 22.774 distance: 157 - 158: 38.659 distance: 158 - 159: 6.417 distance: 159 - 160: 8.841 distance: 160 - 161: 7.821 distance: 160 - 162: 6.935 distance: 163 - 164: 14.443 distance: 164 - 165: 19.584 distance: 164 - 167: 14.443 distance: 165 - 166: 29.306 distance: 167 - 168: 18.325 distance: 167 - 169: 7.167 distance: 170 - 171: 22.537 distance: 171 - 172: 7.895 distance: 171 - 174: 32.737 distance: 172 - 173: 42.317 distance: 172 - 179: 19.659 distance: 174 - 175: 28.322 distance: 175 - 176: 9.498 distance: 176 - 177: 7.390 distance: 177 - 178: 4.525 distance: 179 - 180: 30.883 distance: 180 - 181: 33.512 distance: 180 - 183: 26.969 distance: 181 - 182: 41.558 distance: 181 - 187: 16.404 distance: 183 - 184: 34.868 distance: 184 - 185: 27.044 distance: 184 - 186: 32.215 distance: 187 - 188: 7.632 distance: 188 - 191: 48.845 distance: 189 - 190: 29.552 distance: 189 - 195: 24.442 distance: 191 - 192: 23.795 distance: 192 - 193: 33.984 distance: 192 - 194: 17.644