Starting phenix.real_space_refine on Tue Dec 12 02:27:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gak_3227/12_2023/5gak_3227_neut_updated.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3596 5.49 5 S 105 5.16 5 C 67230 2.51 5 N 23811 2.21 5 O 34233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ARG 32": "NH1" <-> "NH2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 125": "NH1" <-> "NH2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 121": "NH1" <-> "NH2" Residue "b PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 84": "NH1" <-> "NH2" Residue "b TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "e TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "f ARG 70": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "h TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 105": "NH1" <-> "NH2" Residue "j TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "k TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 23": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "n TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "o TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 23": "NH1" <-> "NH2" Residue "q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 155": "NH1" <-> "NH2" Residue "q ASP 157": "OD1" <-> "OD2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 56": "NH1" <-> "NH2" Residue "R PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 128": "NH1" <-> "NH2" Residue "R ARG 175": "NH1" <-> "NH2" Residue "R ARG 181": "NH1" <-> "NH2" Residue "S TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 176": "NH1" <-> "NH2" Residue "S ARG 178": "NH1" <-> "NH2" Residue "S PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 108": "OD1" <-> "OD2" Residue "s ARG 109": "NH1" <-> "NH2" Residue "s ARG 152": "NH1" <-> "NH2" Residue "s ARG 153": "NH1" <-> "NH2" Residue "s ARG 177": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "U TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "U PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 139": "NH1" <-> "NH2" Residue "W TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 128975 Number of models: 1 Model: "" Number of chains: 50 Chain: "1" Number of atoms: 67695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3165, 67695 Classifications: {'RNA': 3165} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 77, 'rna3p_pur': 1628, 'rna3p_pyr': 1335} Link IDs: {'rna2p': 202, 'rna3p': 2962} Chain breaks: 3 Chain: "X" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 60, 'rna3p_pyr': 57} Link IDs: {'rna2p': 4, 'rna3p': 116} Chain: "Y" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 699 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 71, 'rna3p_pyr': 76} Link IDs: {'rna2p': 11, 'rna3p': 146} Chain: "Z" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1611 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 35, 'rna3p_pyr': 38} Link IDs: {'rna2p': 3, 'rna3p': 72} Chain: "a" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 36, 'rna3p_pyr': 38} Link IDs: {'rna2p': 3, 'rna3p': 73} Chain: "b" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "c" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "E" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "F" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "h" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "i" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "j" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "K" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "L" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "l" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "M" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "m" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "n" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "o" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "P" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "p" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "Q" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "q" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1143 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, '5CT:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "S" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "s" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain: "U" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "V" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "W" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "z" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'3HE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 50.33, per 1000 atoms: 0.39 Number of scatterers: 128975 At special positions: 0 Unit cell: (255.824, 214.632, 256.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 3596 15.00 O 34233 8.00 N 23811 7.00 C 67230 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=0, symmetry=0 Time building additional restraints: 58.05 Conformation dependent library (CDL) restraints added in 8.0 seconds 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12460 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: 215 helices and 56 sheets defined 40.0% alpha, 12.7% beta 1076 base pairs and 1437 stacking pairs defined. Time for finding SS restraints: 65.88 Creating SS restraints... Processing helix chain 'X' and resid 66 through 71 removed outlier: 3.984A pdb=" N ARG X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS X 71 " --> pdb=" O PRO X 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 66 through 71' Processing helix chain 'X' and resid 119 through 127 removed outlier: 3.511A pdb=" N ALA X 123 " --> pdb=" O GLY X 119 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU X 125 " --> pdb=" O GLU X 121 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP X 126 " --> pdb=" O CYS X 122 " (cutoff:3.500A) Proline residue: X 127 - end of helix Processing helix chain 'X' and resid 128 through 133 removed outlier: 4.125A pdb=" N ASN X 132 " --> pdb=" O ARG X 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 43 removed outlier: 3.674A pdb=" N LYS Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN Y 42 " --> pdb=" O SER Y 38 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 50 removed outlier: 3.718A pdb=" N ILE Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA Y 50 " --> pdb=" O PRO Y 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 50' Processing helix chain 'Y' and resid 52 through 60 removed outlier: 3.605A pdb=" N ARG Y 56 " --> pdb=" O THR Y 52 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS Y 60 " --> pdb=" O ARG Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.254A pdb=" N ALA Y 68 " --> pdb=" O THR Y 64 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 86 through 93 removed outlier: 4.815A pdb=" N ILE Y 90 " --> pdb=" O SER Y 86 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU Y 92 " --> pdb=" O ASP Y 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 64 removed outlier: 3.810A pdb=" N ILE Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLU Z 64 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 79 removed outlier: 3.906A pdb=" N MET Z 73 " --> pdb=" O SER Z 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP Z 78 " --> pdb=" O LYS Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 103 removed outlier: 3.649A pdb=" N LYS Z 97 " --> pdb=" O TYR Z 93 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA Z 98 " --> pdb=" O GLN Z 94 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS Z 100 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 140 removed outlier: 4.141A pdb=" N ASN Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.553A pdb=" N ALA a 15 " --> pdb=" O ASP a 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA a 18 " --> pdb=" O LYS a 14 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA a 22 " --> pdb=" O ALA a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 32 removed outlier: 3.547A pdb=" N ARG a 28 " --> pdb=" O SER a 24 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU a 30 " --> pdb=" O GLN a 26 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER a 32 " --> pdb=" O ARG a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 44 removed outlier: 3.633A pdb=" N ALA a 41 " --> pdb=" O LYS a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 105 removed outlier: 4.180A pdb=" N LEU a 104 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL a 105 " --> pdb=" O PRO a 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 100 through 105' Processing helix chain 'a' and resid 112 through 123 removed outlier: 5.615A pdb=" N LYS a 116 " --> pdb=" O ASP a 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE a 119 " --> pdb=" O ARG a 115 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS a 122 " --> pdb=" O LEU a 118 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY a 123 " --> pdb=" O ILE a 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 67 removed outlier: 4.279A pdb=" N VAL b 62 " --> pdb=" O GLY b 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG b 65 " --> pdb=" O LYS b 61 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS b 67 " --> pdb=" O ALA b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 81 removed outlier: 3.838A pdb=" N LEU b 80 " --> pdb=" O ASN b 76 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU b 81 " --> pdb=" O TYR b 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 76 through 81' Processing helix chain 'b' and resid 97 through 102 removed outlier: 3.544A pdb=" N PHE b 101 " --> pdb=" O SER b 97 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU b 102 " --> pdb=" O THR b 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 97 through 102' Processing helix chain 'b' and resid 103 through 125 removed outlier: 4.022A pdb=" N GLU b 108 " --> pdb=" O PRO b 104 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA b 110 " --> pdb=" O GLN b 106 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS b 111 " --> pdb=" O ARG b 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG b 121 " --> pdb=" O ALA b 117 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 133 removed outlier: 3.650A pdb=" N SER b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYS b 133 " --> pdb=" O TRP b 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.847A pdb=" N TYR C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.585A pdb=" N LYS c 10 " --> pdb=" O THR c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 48 removed outlier: 4.692A pdb=" N LYS c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 69 removed outlier: 3.876A pdb=" N PHE c 68 " --> pdb=" O GLN c 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 83 removed outlier: 3.578A pdb=" N LEU c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP c 79 " --> pdb=" O LEU c 75 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR c 80 " --> pdb=" O ASP c 76 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU c 81 " --> pdb=" O LYS c 77 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE c 82 " --> pdb=" O LEU c 78 " (cutoff:3.500A) Proline residue: c 83 - end of helix No H-bonds generated for 'chain 'c' and resid 74 through 83' Processing helix chain 'c' and resid 84 through 94 removed outlier: 4.440A pdb=" N ASP c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN c 89 " --> pdb=" O ASP c 85 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA c 94 " --> pdb=" O TYR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 108 removed outlier: 3.731A pdb=" N ALA c 107 " --> pdb=" O ASP c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 142 removed outlier: 4.062A pdb=" N GLU c 136 " --> pdb=" O LYS c 132 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS c 137 " --> pdb=" O LEU c 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 34 removed outlier: 4.150A pdb=" N ARG D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 92 removed outlier: 4.476A pdb=" N THR D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 removed outlier: 4.654A pdb=" N LYS d 15 " --> pdb=" O ASN d 11 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS d 17 " --> pdb=" O THR d 13 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 59 removed outlier: 3.795A pdb=" N HIS d 45 " --> pdb=" O ARG d 41 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA d 46 " --> pdb=" O ASN d 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU d 47 " --> pdb=" O HIS d 43 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS d 52 " --> pdb=" O HIS d 48 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA d 53 " --> pdb=" O GLY d 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYS d 58 " --> pdb=" O LEU d 54 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS d 59 " --> pdb=" O ALA d 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 4.071A pdb=" N GLY E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 39 removed outlier: 4.167A pdb=" N GLY E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.344A pdb=" N VAL E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Proline residue: E 108 - end of helix No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.838A pdb=" N ALA E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 4.026A pdb=" N MET E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASN E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 205' Processing helix chain 'e' and resid 9 through 20 removed outlier: 5.542A pdb=" N LYS e 13 " --> pdb=" O SER e 9 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 16 " --> pdb=" O GLN e 12 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS e 19 " --> pdb=" O ALA e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 37 removed outlier: 3.557A pdb=" N ARG e 35 " --> pdb=" O VAL e 31 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN e 36 " --> pdb=" O LYS e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 64 removed outlier: 4.041A pdb=" N ALA e 60 " --> pdb=" O LEU e 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU e 62 " --> pdb=" O TYR e 58 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER e 63 " --> pdb=" O TYR e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 82 removed outlier: 3.664A pdb=" N GLY e 82 " --> pdb=" O GLY e 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.690A pdb=" N PHE F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 removed outlier: 4.452A pdb=" N LYS F 136 " --> pdb=" O LYS F 132 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TYR F 137 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLN F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 165 through 170 removed outlier: 3.812A pdb=" N THR F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix No H-bonds generated for 'chain 'F' and resid 165 through 170' Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 204 through 209 removed outlier: 4.289A pdb=" N VAL F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.810A pdb=" N ARG F 232 " --> pdb=" O GLY F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 7.232A pdb=" N LEU F 351 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 347 through 352' Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'f' and resid 15 through 21 removed outlier: 4.040A pdb=" N ARG f 19 " --> pdb=" O ASN f 15 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS f 21 " --> pdb=" O HIS f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 44 removed outlier: 3.612A pdb=" N VAL f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS f 38 " --> pdb=" O LYS f 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS f 43 " --> pdb=" O PHE f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 61 removed outlier: 3.506A pdb=" N ASN f 56 " --> pdb=" O ALA f 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP f 60 " --> pdb=" O ASN f 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS f 61 " --> pdb=" O GLN f 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.641A pdb=" N ALA G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix No H-bonds generated for 'chain 'G' and resid 24 through 29' Processing helix chain 'G' and resid 31 through 43 Processing helix chain 'G' and resid 114 through 130 removed outlier: 4.519A pdb=" N ALA G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.591A pdb=" N VAL G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.757A pdb=" N SER G 158 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 161 through 173 removed outlier: 3.733A pdb=" N GLY G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 185 removed outlier: 3.867A pdb=" N VAL G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 184 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS G 185 " --> pdb=" O VAL G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.481A pdb=" N ARG G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 214 through 220 removed outlier: 3.683A pdb=" N ARG G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 Proline residue: G 240 - end of helix Processing helix chain 'G' and resid 251 through 262 removed outlier: 3.986A pdb=" N ASP G 259 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 292 removed outlier: 4.737A pdb=" N ILE G 289 " --> pdb=" O ASP G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 300 removed outlier: 4.302A pdb=" N SER G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA G 298 " --> pdb=" O GLU G 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG G 300 " --> pdb=" O GLN G 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 293 through 300' Processing helix chain 'G' and resid 320 through 328 removed outlier: 3.678A pdb=" N LEU G 324 " --> pdb=" O ASN G 320 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 338 removed outlier: 4.461A pdb=" N VAL G 333 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 361 removed outlier: 3.758A pdb=" N THR G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS G 361 " --> pdb=" O GLU G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 5.561A pdb=" N GLN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR G 60 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER G 61 " --> pdb=" O HIS G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 61' Processing helix chain 'g' and resid 21 through 26 removed outlier: 5.182A pdb=" N HIS g 26 " --> pdb=" O SER g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 45 removed outlier: 3.877A pdb=" N ARG g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG g 45 " --> pdb=" O VAL g 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 40 through 45' Processing helix chain 'g' and resid 78 through 87 removed outlier: 4.131A pdb=" N LEU g 82 " --> pdb=" O ASN g 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR g 84 " --> pdb=" O LYS g 80 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU g 85 " --> pdb=" O ASP g 81 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR g 86 " --> pdb=" O LEU g 82 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET g 87 " --> pdb=" O GLU g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 116 removed outlier: 4.328A pdb=" N VAL g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA g 114 " --> pdb=" O ALA g 110 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU g 115 " --> pdb=" O ARG g 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.639A pdb=" N ARG H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 26 Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.298A pdb=" N ARG H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 removed outlier: 4.609A pdb=" N TYR H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 87' Processing helix chain 'H' and resid 94 through 114 removed outlier: 3.780A pdb=" N GLY H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 removed outlier: 4.704A pdb=" N TYR H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 115 through 120' Processing helix chain 'H' and resid 157 through 170 removed outlier: 3.717A pdb=" N GLY H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY H 170 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 201 removed outlier: 3.925A pdb=" N LEU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 214 removed outlier: 3.578A pdb=" N ASP H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 224 removed outlier: 4.008A pdb=" N PHE H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 223 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 251 removed outlier: 4.536A pdb=" N GLU H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP H 238 " --> pdb=" O ASP H 234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 243 " --> pdb=" O ILE H 239 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Proline residue: H 251 - end of helix Processing helix chain 'H' and resid 261 through 274 removed outlier: 4.024A pdb=" N LYS H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG H 273 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN H 274 " --> pdb=" O LYS H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 293 Processing helix chain 'h' and resid 37 through 42 Processing helix chain 'I' and resid 80 through 85 removed outlier: 4.084A pdb=" N VAL I 84 " --> pdb=" O ASN I 80 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 80 through 85' Processing helix chain 'I' and resid 102 through 107 removed outlier: 3.977A pdb=" N PHE I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA I 107 " --> pdb=" O VAL I 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 102 through 107' Processing helix chain 'I' and resid 131 through 150 removed outlier: 4.135A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 removed outlier: 5.736A pdb=" N SER I 162 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing helix chain 'i' and resid 58 through 66 removed outlier: 3.903A pdb=" N TYR i 62 " --> pdb=" O ARG i 58 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA i 63 " --> pdb=" O PRO i 59 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR i 64 " --> pdb=" O ARG i 60 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL i 65 " --> pdb=" O GLN i 61 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER i 66 " --> pdb=" O TYR i 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 58 through 66' Processing helix chain 'i' and resid 81 through 113 removed outlier: 4.377A pdb=" N VAL i 85 " --> pdb=" O CYS i 81 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA i 92 " --> pdb=" O ARG i 88 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS i 102 " --> pdb=" O GLN i 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS i 106 " --> pdb=" O LYS i 102 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS i 113 " --> pdb=" O THR i 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 73 removed outlier: 5.098A pdb=" N ARG J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 120 through 131 Processing helix chain 'J' and resid 140 through 150 removed outlier: 3.760A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.243A pdb=" N ILE J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.635A pdb=" N THR J 190 " --> pdb=" O HIS J 186 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 203 removed outlier: 5.786A pdb=" N TRP J 203 " --> pdb=" O ASN J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 removed outlier: 4.632A pdb=" N ASN J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS J 238 " --> pdb=" O GLU J 234 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 12 removed outlier: 3.659A pdb=" N LEU j 9 " --> pdb=" O LYS j 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR j 11 " --> pdb=" O TYR j 7 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS j 12 " --> pdb=" O GLU j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 39 removed outlier: 3.764A pdb=" N ALA j 18 " --> pdb=" O LYS j 14 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER j 19 " --> pdb=" O GLU j 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP j 23 " --> pdb=" O SER j 19 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU j 27 " --> pdb=" O ASP j 23 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU j 28 " --> pdb=" O LEU j 24 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA j 29 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU j 36 " --> pdb=" O LYS j 32 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER j 37 " --> pdb=" O VAL j 33 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG j 38 " --> pdb=" O GLN j 34 " (cutoff:3.500A) Proline residue: j 39 - end of helix Processing helix chain 'j' and resid 42 through 71 removed outlier: 4.721A pdb=" N THR j 46 " --> pdb=" O PRO j 42 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL j 47 " --> pdb=" O LYS j 43 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG j 48 " --> pdb=" O ILE j 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN j 61 " --> pdb=" O VAL j 57 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL j 66 " --> pdb=" O GLN j 62 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU j 69 " --> pdb=" O ALA j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 82 removed outlier: 5.638A pdb=" N ALA j 82 " --> pdb=" O LYS j 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 85 through 91 removed outlier: 3.766A pdb=" N ALA j 91 " --> pdb=" O ALA j 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 100 removed outlier: 6.583A pdb=" N VAL j 100 " --> pdb=" O GLU j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 101 through 111 removed outlier: 3.990A pdb=" N LYS j 107 " --> pdb=" O LYS j 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 69 removed outlier: 3.780A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 removed outlier: 4.691A pdb=" N ALA K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN K 77 " --> pdb=" O PRO K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 77' Processing helix chain 'K' and resid 83 through 98 removed outlier: 3.549A pdb=" N ALA K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS K 96 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR K 97 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG K 98 " --> pdb=" O PHE K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 119 removed outlier: 4.095A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 removed outlier: 3.939A pdb=" N ASN K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 174 removed outlier: 4.686A pdb=" N VAL K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N PHE K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) Proline residue: K 167 - end of helix Processing helix chain 'K' and resid 182 through 191 removed outlier: 4.865A pdb=" N LEU K 186 " --> pdb=" O GLY K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 222 removed outlier: 3.720A pdb=" N ALA K 212 " --> pdb=" O GLU K 208 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 233 removed outlier: 3.637A pdb=" N HIS K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TRP K 233 " --> pdb=" O VAL K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 255 removed outlier: 3.570A pdb=" N ASP K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 removed outlier: 5.143A pdb=" N ALA K 125 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER K 126 " --> pdb=" O GLN K 123 " (cutoff:3.500A) Proline residue: K 127 - end of helix No H-bonds generated for 'chain 'K' and resid 122 through 127' Processing helix chain 'k' and resid 34 through 49 removed outlier: 4.677A pdb=" N LYS k 38 " --> pdb=" O SER k 34 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE k 39 " --> pdb=" O ASN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 64 removed outlier: 4.243A pdb=" N LEU k 60 " --> pdb=" O ARG k 56 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG k 62 " --> pdb=" O ILE k 58 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN k 63 " --> pdb=" O ASP k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 77 removed outlier: 3.506A pdb=" N ALA k 69 " --> pdb=" O GLY k 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG k 70 " --> pdb=" O GLU k 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS k 71 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG k 76 " --> pdb=" O VAL k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 97 removed outlier: 4.218A pdb=" N ALA k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET k 90 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN k 91 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN k 92 " --> pdb=" O GLU k 88 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER k 97 " --> pdb=" O ILE k 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 32 removed outlier: 5.177A pdb=" N LYS k 30 " --> pdb=" O SER k 27 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY k 31 " --> pdb=" O TYR k 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 84 removed outlier: 3.676A pdb=" N THR L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 166 removed outlier: 3.964A pdb=" N CYS L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 176 removed outlier: 3.615A pdb=" N PHE L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 171 through 176' Processing helix chain 'l' and resid 4 through 12 removed outlier: 4.060A pdb=" N PHE l 8 " --> pdb=" O GLY l 4 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS l 10 " --> pdb=" O PRO l 6 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG l 11 " --> pdb=" O SER l 7 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N HIS l 12 " --> pdb=" O PHE l 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 12' Processing helix chain 'l' and resid 50 through 58 removed outlier: 4.157A pdb=" N LYS l 54 " --> pdb=" O GLY l 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS l 57 " --> pdb=" O ALA l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 65 through 77 removed outlier: 6.096A pdb=" N HIS l 69 " --> pdb=" O ARG l 65 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER l 71 " --> pdb=" O LEU l 67 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG l 72 " --> pdb=" O LYS l 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG l 73 " --> pdb=" O HIS l 69 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN l 76 " --> pdb=" O ARG l 72 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY l 77 " --> pdb=" O ARG l 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 41 removed outlier: 4.020A pdb=" N THR M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 88 removed outlier: 4.462A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 removed outlier: 4.591A pdb=" N LEU M 112 " --> pdb=" O GLU M 108 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY M 113 " --> pdb=" O HIS M 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 108 through 113' Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.681A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 167 removed outlier: 4.169A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS M 166 " --> pdb=" O TRP M 162 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR M 167 " --> pdb=" O PHE M 163 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 18 removed outlier: 4.098A pdb=" N ARG m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG m 17 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA m 18 " --> pdb=" O LEU m 14 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 69 removed outlier: 3.683A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS m 64 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN m 67 " --> pdb=" O LYS m 63 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER m 68 " --> pdb=" O LYS m 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 47 removed outlier: 4.520A pdb=" N LYS N 31 " --> pdb=" O ASP N 27 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 4.730A pdb=" N VAL N 80 " --> pdb=" O THR N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 94 removed outlier: 3.671A pdb=" N GLY N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 124 removed outlier: 3.533A pdb=" N ILE N 123 " --> pdb=" O TYR N 119 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE N 124 " --> pdb=" O GLN N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 146 removed outlier: 5.511A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 165 through 180 removed outlier: 4.621A pdb=" N THR N 169 " --> pdb=" O SER N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 193 removed outlier: 4.064A pdb=" N ALA N 187 " --> pdb=" O ARG N 183 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA N 193 " --> pdb=" O GLU N 189 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 21 removed outlier: 3.940A pdb=" N ALA n 14 " --> pdb=" O LYS n 10 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS n 15 " --> pdb=" O GLN n 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN n 20 " --> pdb=" O ALA n 16 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ARG n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.458A pdb=" N ARG n 28 " --> pdb=" O PRO n 24 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU n 29 " --> pdb=" O GLN n 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG n 30 " --> pdb=" O TRP n 26 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR n 31 " --> pdb=" O ILE n 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 24 through 31' Processing helix chain 'O' and resid 59 through 64 removed outlier: 3.805A pdb=" N VAL O 63 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 59 through 64' Processing helix chain 'O' and resid 77 through 89 removed outlier: 3.609A pdb=" N LYS O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA O 88 " --> pdb=" O LYS O 84 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA O 89 " --> pdb=" O TRP O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 removed outlier: 5.761A pdb=" N SER O 98 " --> pdb=" O TRP O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 3.832A pdb=" N ALA O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU O 112 " --> pdb=" O ARG O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 137 removed outlier: 3.624A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 90 removed outlier: 5.258A pdb=" N LEU o 85 " --> pdb=" O SER o 81 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA o 86 " --> pdb=" O LEU o 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER o 87 " --> pdb=" O LYS o 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS o 88 " --> pdb=" O ALA o 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR o 89 " --> pdb=" O LEU o 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.644A pdb=" N LEU P 7 " --> pdb=" O ALA P 3 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG P 12 " --> pdb=" O GLU P 8 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 34 removed outlier: 3.803A pdb=" N LEU P 22 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG P 24 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP P 28 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN P 32 " --> pdb=" O TRP P 28 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASN P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 52 removed outlier: 4.007A pdb=" N LEU P 51 " --> pdb=" O LYS P 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 88 removed outlier: 4.057A pdb=" N GLN P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 83 through 88' Processing helix chain 'P' and resid 97 through 111 removed outlier: 4.033A pdb=" N GLU P 103 " --> pdb=" O ARG P 99 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG P 108 " --> pdb=" O GLU P 104 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA P 111 " --> pdb=" O GLY P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 145 removed outlier: 3.542A pdb=" N ARG P 143 " --> pdb=" O HIS P 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG P 144 " --> pdb=" O LYS P 140 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP P 145 " --> pdb=" O ALA P 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 139 through 145' Processing helix chain 'P' and resid 146 through 154 removed outlier: 4.677A pdb=" N TRP P 150 " --> pdb=" O ALA P 146 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE P 151 " --> pdb=" O ARG P 147 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS P 152 " --> pdb=" O TYR P 148 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP P 153 " --> pdb=" O ASN P 149 " (cutoff:3.500A) Proline residue: P 154 - end of helix No H-bonds generated for 'chain 'P' and resid 146 through 154' Processing helix chain 'P' and resid 158 through 163 removed outlier: 3.687A pdb=" N ARG P 162 " --> pdb=" O HIS P 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY P 163 " --> pdb=" O ARG P 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 158 through 163' Processing helix chain 'P' and resid 165 through 173 removed outlier: 3.881A pdb=" N LYS P 170 " --> pdb=" O ALA P 166 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY P 173 " --> pdb=" O LYS P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 196 removed outlier: 3.924A pdb=" N LYS P 192 " --> pdb=" O ARG P 188 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN P 194 " --> pdb=" O THR P 190 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 25 removed outlier: 4.445A pdb=" N LYS p 8 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG p 9 " --> pdb=" O TRP p 5 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR p 10 " --> pdb=" O ARG p 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU p 13 " --> pdb=" O ARG p 9 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS p 19 " --> pdb=" O ARG p 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS p 25 " --> pdb=" O ARG p 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 30 removed outlier: 3.582A pdb=" N ALA Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY Q 30 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.775A pdb=" N ASN Q 50 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP Q 56 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA Q 61 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 89 removed outlier: 3.508A pdb=" N ILE Q 79 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE Q 80 " --> pdb=" O PRO Q 76 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 103 removed outlier: 3.990A pdb=" N LYS Q 96 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Q 99 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU Q 100 " --> pdb=" O LYS Q 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 116 removed outlier: 3.802A pdb=" N ASP Q 113 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS Q 114 " --> pdb=" O PRO Q 110 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS Q 115 " --> pdb=" O PRO Q 111 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS Q 116 " --> pdb=" O TYR Q 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 109 through 116' Processing helix chain 'Q' and resid 124 through 129 removed outlier: 3.669A pdb=" N LEU Q 129 " --> pdb=" O ARG Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 removed outlier: 3.655A pdb=" N SER Q 144 " --> pdb=" O LYS Q 140 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY Q 146 " --> pdb=" O SER Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 187 removed outlier: 4.677A pdb=" N VAL Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER Q 180 " --> pdb=" O LYS Q 176 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA Q 186 " --> pdb=" O ASN Q 182 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU Q 187 " --> pdb=" O ALA Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 198 removed outlier: 3.652A pdb=" N GLN Q 193 " --> pdb=" O ASP Q 189 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA Q 195 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) Processing helix chain 'q' and resid 118 through 129 removed outlier: 3.936A pdb=" N SER q 123 " --> pdb=" O GLU q 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU q 124 " --> pdb=" O LEU q 120 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASP q 129 " --> pdb=" O GLN q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 15 removed outlier: 5.526A pdb=" N ALA R 15 " --> pdb=" O PRO R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 4.405A pdb=" N GLU R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.537A pdb=" N ALA R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS R 54 " --> pdb=" O GLN R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 106 removed outlier: 3.986A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 94 " --> pdb=" O PHE R 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN R 97 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS R 105 " --> pdb=" O ASN R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 183 removed outlier: 4.032A pdb=" N ARG R 175 " --> pdb=" O ARG R 171 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE R 176 " --> pdb=" O GLN R 172 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS R 180 " --> pdb=" O ILE R 176 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE R 182 " --> pdb=" O ALA R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 removed outlier: 3.699A pdb=" N GLY R 73 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU R 75 " --> pdb=" O GLN R 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 40 removed outlier: 3.920A pdb=" N LEU S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL S 30 " --> pdb=" O LEU S 26 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE S 35 " --> pdb=" O LYS S 31 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG S 39 " --> pdb=" O PHE S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 54 removed outlier: 3.779A pdb=" N LYS S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU S 49 " --> pdb=" O ASN S 45 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 Proline residue: S 60 - end of helix Processing helix chain 'S' and resid 63 through 74 removed outlier: 3.533A pdb=" N ILE S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG S 69 " --> pdb=" O SER S 65 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU S 74 " --> pdb=" O ALA S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 118 removed outlier: 3.719A pdb=" N ALA S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS S 116 " --> pdb=" O ALA S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 131 removed outlier: 3.556A pdb=" N VAL S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG S 130 " --> pdb=" O GLN S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 153 removed outlier: 4.806A pdb=" N HIS S 152 " --> pdb=" O GLU S 148 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE S 153 " --> pdb=" O ALA S 149 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 4.305A pdb=" N PHE s 45 " --> pdb=" O THR s 41 " (cutoff:3.500A) Proline residue: s 46 - end of helix No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 60 through 79 removed outlier: 3.538A pdb=" N LEU s 64 " --> pdb=" O SER s 60 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG s 68 " --> pdb=" O LEU s 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN s 72 " --> pdb=" O ARG s 68 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL s 78 " --> pdb=" O TYR s 74 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 159 removed outlier: 3.941A pdb=" N LYS s 144 " --> pdb=" O LYS s 140 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP s 145 " --> pdb=" O ASP s 141 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL s 146 " --> pdb=" O SER s 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL s 148 " --> pdb=" O LYS s 144 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU s 149 " --> pdb=" O ASP s 145 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA s 154 " --> pdb=" O GLY s 150 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR s 156 " --> pdb=" O ARG s 152 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS s 157 " --> pdb=" O ARG s 153 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE s 158 " --> pdb=" O ALA s 154 " (cutoff:3.500A) Proline residue: s 159 - end of helix Processing helix chain 's' and resid 177 through 187 removed outlier: 3.525A pdb=" N GLU s 185 " --> pdb=" O LEU s 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA s 186 " --> pdb=" O LYS s 182 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 212 removed outlier: 3.565A pdb=" N ASN s 208 " --> pdb=" O SER s 204 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE s 209 " --> pdb=" O LEU s 205 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG s 210 " --> pdb=" O GLU s 206 " (cutoff:3.500A) Processing helix chain 's' and resid 213 through 218 removed outlier: 3.719A pdb=" N ALA s 217 " --> pdb=" O PRO s 213 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA s 218 " --> pdb=" O GLU s 214 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 213 through 218' Processing helix chain 'T' and resid 4 through 16 removed outlier: 3.744A pdb=" N ARG T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA T 11 " --> pdb=" O GLN T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 36 removed outlier: 5.388A pdb=" N SER T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU T 31 " --> pdb=" O ASN T 27 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN T 34 " --> pdb=" O SER T 30 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 4.005A pdb=" N LYS T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY T 48 " --> pdb=" O LEU T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 4.973A pdb=" N ARG T 64 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER T 69 " --> pdb=" O ALA T 65 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS T 70 " --> pdb=" O HIS T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 4.561A pdb=" N LYS T 82 " --> pdb=" O TYR T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 113 removed outlier: 3.816A pdb=" N LEU T 89 " --> pdb=" O ARG T 85 " (cutoff:3.500A) Proline residue: T 90 - end of helix removed outlier: 6.114A pdb=" N VAL T 93 " --> pdb=" O LEU T 89 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE T 96 " --> pdb=" O GLN T 92 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU T 99 " --> pdb=" O TRP T 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL T 101 " --> pdb=" O ARG T 97 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU T 102 " --> pdb=" O ARG T 98 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG T 104 " --> pdb=" O ARG T 100 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA T 107 " --> pdb=" O ARG T 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS T 108 " --> pdb=" O ARG T 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR T 109 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP T 111 " --> pdb=" O ALA T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 130 removed outlier: 4.111A pdb=" N LYS T 125 " --> pdb=" O HIS T 121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU T 126 " --> pdb=" O VAL T 122 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS T 128 " --> pdb=" O TYR T 124 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN T 130 " --> pdb=" O GLU T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 188 removed outlier: 3.603A pdb=" N GLU T 140 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS T 141 " --> pdb=" O ALA T 137 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN T 144 " --> pdb=" O GLU T 140 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA T 145 " --> pdb=" O HIS T 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA T 149 " --> pdb=" O ALA T 145 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN T 150 " --> pdb=" O LYS T 146 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA T 159 " --> pdb=" O LEU T 155 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU T 160 " --> pdb=" O ASN T 156 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG T 163 " --> pdb=" O ALA T 159 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG T 167 " --> pdb=" O ARG T 163 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA T 168 " --> pdb=" O LEU T 164 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA T 169 " --> pdb=" O LYS T 165 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG T 170 " --> pdb=" O ASN T 166 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA T 174 " --> pdb=" O ARG T 170 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL T 177 " --> pdb=" O ARG T 173 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU T 179 " --> pdb=" O GLN T 175 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS T 180 " --> pdb=" O ARG T 176 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP T 182 " --> pdb=" O ALA T 178 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA T 183 " --> pdb=" O GLU T 179 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU T 184 " --> pdb=" O LYS T 180 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU T 185 " --> pdb=" O ARG T 181 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 49 removed outlier: 3.565A pdb=" N ALA U 37 " --> pdb=" O ASN U 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE U 44 " --> pdb=" O ARG U 40 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU U 45 " --> pdb=" O TYR U 41 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS U 47 " --> pdb=" O TYR U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 114 removed outlier: 3.929A pdb=" N GLU U 104 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA U 112 " --> pdb=" O GLN U 108 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS U 114 " --> pdb=" O MET U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 122 removed outlier: 3.778A pdb=" N ILE U 121 " --> pdb=" O ARG U 117 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS U 122 " --> pdb=" O PHE U 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 117 through 122' Processing helix chain 'U' and resid 137 through 145 removed outlier: 4.880A pdb=" N PHE U 143 " --> pdb=" O TYR U 139 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU U 144 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR U 145 " --> pdb=" O LYS U 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 16 removed outlier: 4.223A pdb=" N GLN V 16 " --> pdb=" O ARG V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 27 through 32 removed outlier: 3.754A pdb=" N LEU V 31 " --> pdb=" O LEU V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 97 removed outlier: 4.308A pdb=" N ILE V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS V 97 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 92 through 97' Processing helix chain 'V' and resid 99 through 123 removed outlier: 4.015A pdb=" N GLN V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA V 113 " --> pdb=" O VAL V 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA V 114 " --> pdb=" O LYS V 110 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU V 118 " --> pdb=" O ALA V 114 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA V 119 " --> pdb=" O LYS V 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS V 120 " --> pdb=" O ARG V 116 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA V 121 " --> pdb=" O ALA V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 26 removed outlier: 3.510A pdb=" N ASN W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 41 removed outlier: 3.728A pdb=" N TYR W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA W 34 " --> pdb=" O PRO W 30 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS W 40 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE W 41 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 88 removed outlier: 3.811A pdb=" N LYS W 85 " --> pdb=" O LYS W 81 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS W 86 " --> pdb=" O LYS W 82 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN W 87 " --> pdb=" O TYR W 83 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'X' and resid 82 through 87 removed outlier: 6.789A pdb=" N LYS X 83 " --> pdb=" O TYR X 94 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR X 94 " --> pdb=" O LYS X 83 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TRP X 85 " --> pdb=" O PHE X 92 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE X 92 " --> pdb=" O TRP X 85 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG X 87 " --> pdb=" O GLY X 90 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'X' and resid 21 through 24 removed outlier: 5.436A pdb=" N ALA X 21 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET X 23 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE X 37 " --> pdb=" O MET X 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP X 56 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA X 99 " --> pdb=" O VAL X 79 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'X' and resid 23 through 26 removed outlier: 3.694A pdb=" N ASN X 24 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'Y' and resid 18 through 22 removed outlier: 3.629A pdb=" N PHE Y 21 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'Z' and resid 81 through 86 removed outlier: 3.926A pdb=" N LYS Z 120 " --> pdb=" O VAL Z 86 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'a' and resid 72 through 75 removed outlier: 3.525A pdb=" N SER a 72 " --> pdb=" O GLN a 81 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'b' and resid 10 through 14 removed outlier: 4.226A pdb=" N LYS b 21 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'b' and resid 27 through 30 removed outlier: 3.960A pdb=" N LYS b 27 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU b 42 " --> pdb=" O LYS b 27 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 23 through 28 removed outlier: 6.416A pdb=" N VAL C 69 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 53 through 57 removed outlier: 4.556A pdb=" N GLY D 53 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS D 62 " --> pdb=" O CYS D 57 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 47 through 50 removed outlier: 3.957A pdb=" N GLN E 47 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 60 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS E 60 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 44 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN E 86 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.538A pdb=" N LEU E 150 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 58 through 64 Processing sheet with id= 14, first strand: chain 'e' and resid 65 through 71 removed outlier: 4.678A pdb=" N LYS e 66 " --> pdb=" O LYS e 40 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE e 42 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE e 44 " --> pdb=" O TYR e 68 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA e 46 " --> pdb=" O PHE e 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 41 " --> pdb=" O ILE e 92 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 44 through 50 removed outlier: 7.927A pdb=" N THR F 44 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG F 334 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE F 335 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL F 220 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 53 through 59 removed outlier: 4.064A pdb=" N ILE F 56 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 157 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR F 95 " --> pdb=" O GLY F 98 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 284 through 288 removed outlier: 3.719A pdb=" N ARG F 284 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN F 319 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 76 through 82 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'F' and resid 159 through 163 Processing sheet with id= 20, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.658A pdb=" N GLU F 213 " --> pdb=" O ILE F 282 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 48 through 51 removed outlier: 5.413A pdb=" N ASP f 48 " --> pdb=" O LEU f 89 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR f 9 " --> pdb=" O VAL f 109 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL f 107 " --> pdb=" O GLU f 11 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 224 through 229 removed outlier: 3.549A pdb=" N GLU G 226 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE G 247 " --> pdb=" O GLY G 204 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'g' and resid 71 through 77 removed outlier: 3.722A pdb=" N ALA g 93 " --> pdb=" O LYS g 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA g 97 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 60 through 64 removed outlier: 6.836A pdb=" N ILE H 60 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 76 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'h' and resid 11 through 14 removed outlier: 4.280A pdb=" N LEU h 29 " --> pdb=" O LEU h 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG h 82 " --> pdb=" O THR h 72 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS h 63 " --> pdb=" O ALA h 55 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL h 71 " --> pdb=" O LYS h 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS h 47 " --> pdb=" O VAL h 71 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG h 48 " --> pdb=" O PHE h 101 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'h' and resid 8 through 14 removed outlier: 4.298A pdb=" N ALA h 96 " --> pdb=" O HIS h 13 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 63 through 66 Processing sheet with id= 28, first strand: chain 'i' and resid 20 through 24 removed outlier: 3.536A pdb=" N VAL i 23 " --> pdb=" O ARG i 31 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 133 through 138 removed outlier: 7.947A pdb=" N TYR J 133 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS J 82 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER J 113 " --> pdb=" O ARG J 88 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN J 112 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 152 through 155 removed outlier: 9.057A pdb=" N GLY J 152 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 177 through 181 removed outlier: 3.662A pdb=" N ASN K 155 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 5 through 12 removed outlier: 3.615A pdb=" N VAL L 12 " --> pdb=" O GLN L 51 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN L 51 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU L 52 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 16 through 20 Processing sheet with id= 34, first strand: chain 'L' and resid 132 through 137 removed outlier: 3.546A pdb=" N SER L 137 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU L 143 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP L 142 " --> pdb=" O TYR L 92 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.306A pdb=" N ILE M 65 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL M 23 " --> pdb=" O ILE M 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 16 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER M 22 " --> pdb=" O GLY M 124 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY M 124 " --> pdb=" O SER M 22 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'm' and resid 2 through 5 removed outlier: 3.521A pdb=" N ALA m 23 " --> pdb=" O LYS m 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL m 25 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE m 27 " --> pdb=" O LEU m 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 55 through 59 Processing sheet with id= 38, first strand: chain 'O' and resid 19 through 24 removed outlier: 5.132A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'O' and resid 44 through 47 Processing sheet with id= 40, first strand: chain 'o' and resid 100 through 103 removed outlier: 4.084A pdb=" N ALA o 101 " --> pdb=" O CYS o 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG o 97 " --> pdb=" O GLN o 120 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLN o 120 " --> pdb=" O ARG o 97 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 35 through 39 removed outlier: 7.281A pdb=" N VAL P 35 " --> pdb=" O ARG P 65 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE P 61 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY P 58 " --> pdb=" O ASP P 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS P 128 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE P 133 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU P 116 " --> pdb=" O ILE P 133 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 6 through 10 Processing sheet with id= 43, first strand: chain 'q' and resid 30 through 33 removed outlier: 4.872A pdb=" N GLY q 30 " --> pdb=" O ILE q 41 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'q' and resid 42 through 48 removed outlier: 5.169A pdb=" N LYS q 68 " --> pdb=" O ASP q 63 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'q' and resid 89 through 92 removed outlier: 4.142A pdb=" N LEU q 134 " --> pdb=" O LEU q 92 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER q 149 " --> pdb=" O THR q 137 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'R' and resid 111 through 114 removed outlier: 6.521A pdb=" N LYS R 111 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS R 153 " --> pdb=" O LYS R 111 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN R 137 " --> pdb=" O THR R 129 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER R 141 " --> pdb=" O GLN R 125 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN R 125 " --> pdb=" O SER R 141 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 100 through 103 removed outlier: 5.136A pdb=" N THR S 100 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU S 140 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 's' and resid 33 through 36 removed outlier: 6.402A pdb=" N TYR s 33 " --> pdb=" O VAL s 88 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL s 49 " --> pdb=" O VAL s 137 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 's' and resid 94 through 97 removed outlier: 3.916A pdb=" N HIS s 94 " --> pdb=" O ALA s 125 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU s 96 " --> pdb=" O GLY s 123 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY s 123 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 's' and resid 188 through 191 removed outlier: 7.764A pdb=" N GLU s 188 " --> pdb=" O LEU s 199 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS s 190 " --> pdb=" O LYS s 197 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS s 197 " --> pdb=" O LYS s 190 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'U' and resid 24 through 30 removed outlier: 3.552A pdb=" N GLY U 11 " --> pdb=" O PHE U 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE U 10 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU U 57 " --> pdb=" O ARG U 12 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'U' and resid 86 through 96 removed outlier: 3.718A pdb=" N GLY U 86 " --> pdb=" O SER U 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP U 78 " --> pdb=" O LYS U 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS U 125 " --> pdb=" O TRP U 78 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 6 through 10 removed outlier: 3.833A pdb=" N GLU U 6 " --> pdb=" O ILE U 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER U 60 " --> pdb=" O ILE U 10 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 38 through 43 removed outlier: 4.767A pdb=" N ASP V 38 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS V 60 " --> pdb=" O ILE V 42 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 72 through 79 removed outlier: 3.824A pdb=" N VAL V 74 " --> pdb=" O LEU V 89 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 54 through 58 removed outlier: 3.642A pdb=" N SER W 67 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN W 101 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP W 18 " --> pdb=" O TYR W 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU W 105 " --> pdb=" O ASP W 18 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU W 102 " --> pdb=" O THR W 98 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG W 104 " --> pdb=" O VAL W 96 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL W 96 " --> pdb=" O ARG W 104 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 4314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2654 hydrogen bonds 4290 hydrogen bond angles 0 basepair planarities 1076 basepair parallelities 1437 stacking parallelities Total time for adding SS restraints: 160.16 Time building geometry restraints manager: 62.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16154 1.32 - 1.45: 57132 1.45 - 1.57: 58392 1.57 - 1.69: 7186 1.69 - 1.81: 167 Bond restraints: 139031 Sorted by residual: bond pdb=" CD GLN s 112 " pdb=" OE1 GLN s 112 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.61e+01 bond pdb=" CD GLN s 112 " pdb=" NE2 GLN s 112 " ideal model delta sigma weight residual 1.328 1.231 0.097 2.10e-02 2.27e+03 2.13e+01 bond pdb=" CA LYS P 179 " pdb=" C LYS P 179 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.38e-02 5.25e+03 1.65e+01 bond pdb=" CA ARG f 74 " pdb=" CB ARG f 74 " ideal model delta sigma weight residual 1.527 1.479 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" CA THR d 13 " pdb=" C THR d 13 " ideal model delta sigma weight residual 1.522 1.474 0.048 1.43e-02 4.89e+03 1.12e+01 ... (remaining 139026 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.80: 19537 105.80 - 113.24: 83469 113.24 - 120.69: 58618 120.69 - 128.13: 37567 128.13 - 135.58: 6123 Bond angle restraints: 205314 Sorted by residual: angle pdb=" C THR N 62 " pdb=" CA THR N 62 " pdb=" CB THR N 62 " ideal model delta sigma weight residual 115.89 106.34 9.55 1.32e+00 5.74e-01 5.23e+01 angle pdb=" C ARG U 13 " pdb=" CA ARG U 13 " pdb=" CB ARG U 13 " ideal model delta sigma weight residual 115.89 106.62 9.27 1.32e+00 5.74e-01 4.93e+01 angle pdb=" C PHE s 135 " pdb=" CA PHE s 135 " pdb=" CB PHE s 135 " ideal model delta sigma weight residual 115.79 107.57 8.22 1.19e+00 7.06e-01 4.78e+01 angle pdb=" C LEU U 24 " pdb=" CA LEU U 24 " pdb=" CB LEU U 24 " ideal model delta sigma weight residual 115.89 107.16 8.73 1.32e+00 5.74e-01 4.38e+01 angle pdb=" C SER F 38 " pdb=" N LYS F 39 " pdb=" CA LYS F 39 " ideal model delta sigma weight residual 120.86 131.37 -10.51 1.60e+00 3.91e-01 4.32e+01 ... (remaining 205309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 75189 36.00 - 71.99: 8169 71.99 - 107.99: 1037 107.99 - 143.98: 139 143.98 - 179.98: 216 Dihedral angle restraints: 84750 sinusoidal: 65455 harmonic: 19295 Sorted by residual: dihedral pdb=" C5' A 11103 " pdb=" C4' A 11103 " pdb=" C3' A 11103 " pdb=" O3' A 11103 " ideal model delta sinusoidal sigma weight residual 147.00 70.82 76.18 1 8.00e+00 1.56e-02 1.14e+02 dihedral pdb=" CA GLY s 171 " pdb=" C GLY s 171 " pdb=" N PHE s 172 " pdb=" CA PHE s 172 " ideal model delta harmonic sigma weight residual 180.00 126.92 53.08 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" C5' G 12283 " pdb=" C4' G 12283 " pdb=" C3' G 12283 " pdb=" O3' G 12283 " ideal model delta sinusoidal sigma weight residual 147.00 72.76 74.24 1 8.00e+00 1.56e-02 1.09e+02 ... (remaining 84747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 23621 0.088 - 0.175: 1657 0.175 - 0.263: 415 0.263 - 0.350: 152 0.350 - 0.438: 29 Chirality restraints: 25874 Sorted by residual: chirality pdb=" C1' A 11524 " pdb=" O4' A 11524 " pdb=" C2' A 11524 " pdb=" N9 A 11524 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C3' U 11144 " pdb=" C4' U 11144 " pdb=" O3' U 11144 " pdb=" C2' U 11144 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C3' G 12283 " pdb=" C4' G 12283 " pdb=" O3' G 12283 " pdb=" C2' G 12283 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 25871 not shown) Planarity restraints: 12679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 1 82 " 0.006 2.00e-02 2.50e+03 3.24e-02 2.37e+01 pdb=" N1 C 1 82 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C 1 82 " -0.083 2.00e-02 2.50e+03 pdb=" O2 C 1 82 " 0.041 2.00e-02 2.50e+03 pdb=" N3 C 1 82 " 0.025 2.00e-02 2.50e+03 pdb=" C4 C 1 82 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C 1 82 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C 1 82 " 0.013 2.00e-02 2.50e+03 pdb=" C6 C 1 82 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 4 120 " -0.007 2.00e-02 2.50e+03 2.94e-02 1.94e+01 pdb=" N1 C 4 120 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C 4 120 " 0.075 2.00e-02 2.50e+03 pdb=" O2 C 4 120 " -0.040 2.00e-02 2.50e+03 pdb=" N3 C 4 120 " -0.016 2.00e-02 2.50e+03 pdb=" C4 C 4 120 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C 4 120 " 0.001 2.00e-02 2.50e+03 pdb=" C5 C 4 120 " -0.014 2.00e-02 2.50e+03 pdb=" C6 C 4 120 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11403 " 0.013 2.00e-02 2.50e+03 2.94e-02 1.94e+01 pdb=" N1 C 11403 " -0.004 2.00e-02 2.50e+03 pdb=" C2 C 11403 " -0.074 2.00e-02 2.50e+03 pdb=" O2 C 11403 " 0.040 2.00e-02 2.50e+03 pdb=" N3 C 11403 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C 11403 " -0.012 2.00e-02 2.50e+03 pdb=" N4 C 11403 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C 11403 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C 11403 " 0.004 2.00e-02 2.50e+03 ... (remaining 12676 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.63: 3 1.63 - 2.45: 1160 2.45 - 3.27: 145340 3.27 - 4.08: 387261 4.08 - 4.90: 589533 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1123297 Sorted by model distance: nonbonded pdb=" O4 U 12978 " pdb=" CB UNK z 17 " model vdw 0.816 3.440 nonbonded pdb=" O3' A A 76 " pdb=" C UNK z 24 " model vdw 1.353 3.270 nonbonded pdb=" O LYS q 132 " pdb=" OE2 GLU q 152 " model vdw 1.479 3.040 nonbonded pdb=" OP2 C B 74 " pdb=" OD2 ASP s 108 " model vdw 1.659 3.040 nonbonded pdb=" OP2 A 11135 " pdb=" NZ LYS d 5 " model vdw 1.665 2.520 ... (remaining 1123292 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.640 Check model and map are aligned: 1.460 Set scattering table: 0.900 Process input model: 429.950 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 455.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0231 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 : 0.006 0.097 139031 Z= 0.386 Angle : 0.943 14.276 205314 Z= 0.522 Chirality : 0.058 0.438 25874 Planarity : 0.005 0.075 12679 Dihedral : 25.011 179.977 72290 Min Nonbonded Distance : 0.816 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.16 % Favored : 90.18 % Rotamer: Outliers : 0.26 % Allowed : 0.73 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.08), residues: 6345 helix: -3.98 (0.07), residues: 1735 sheet: -2.31 (0.14), residues: 869 loop : -1.83 (0.09), residues: 3741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP O 85 HIS 0.013 0.002 HIS U 114 PHE 0.030 0.003 PHE S 153 TYR 0.034 0.003 TYR R 139 ARG 0.010 0.001 ARG V 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 535 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 549 average time/residue: 1.2889 time to fit residues: 1159.1468 Evaluate side-chains 270 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 6.018 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 1.0270 time to fit residues: 14.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 846 optimal weight: 0.0980 chunk 760 optimal weight: 0.0040 chunk 421 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 786 optimal weight: 0.7980 chunk 304 optimal weight: 10.0000 chunk 478 optimal weight: 10.0000 chunk 585 optimal weight: 0.0060 chunk 910 optimal weight: 4.9990 overall best weight: 1.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 GLN ** b 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 HIS b 127 ASN C 22 GLN C 59 HIS c 44 ASN ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN E 38 HIS E 97 ASN E 132 ASN E 205 ASN E 209 HIS e 11 ASN f 57 GLN G 5 GLN G 114 ASN G 116 ASN G 279 HIS G 296 GLN ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS H 57 ASN h 42 GLN J 159 GLN J 225 GLN K 38 GLN K 59 GLN K 138 HIS L 58 HIS L 125 ASN L 163 GLN l 76 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 HIS M 152 HIS m 40 GLN N 13 HIS ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN P 11 GLN P 15 GLN P 37 HIS P 87 GLN P 117 ASN P 156 HIS P 175 ASN Q 182 ASN q 88 ASN R 145 HIS S 73 GLN s 112 GLN s 143 ASN T 121 HIS T 166 ASN U 108 GLN U 122 HIS U 142 GLN U 157 GLN V 45 ASN ** V 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0451 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 139031 Z= 0.201 Angle : 0.799 12.823 205314 Z= 0.410 Chirality : 0.044 0.384 25874 Planarity : 0.006 0.083 12679 Dihedral : 24.448 179.085 59493 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.83 % Favored : 93.79 % Rotamer: Outliers : 1.24 % Allowed : 4.37 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.09), residues: 6345 helix: -1.89 (0.10), residues: 1908 sheet: -1.80 (0.15), residues: 862 loop : -1.22 (0.10), residues: 3575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 85 HIS 0.013 0.001 HIS K 138 PHE 0.029 0.002 PHE F 370 TYR 0.032 0.002 TYR P 129 ARG 0.011 0.001 ARG b 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 324 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 32 residues processed: 376 average time/residue: 1.2141 time to fit residues: 776.1867 Evaluate side-chains 277 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 6.377 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 1.0150 time to fit residues: 65.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 506 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 758 optimal weight: 8.9990 chunk 620 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 912 optimal weight: 8.9990 chunk 985 optimal weight: 20.0000 chunk 812 optimal weight: 10.0000 chunk 904 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 732 optimal weight: 0.0870 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 45 ASN a 110 HIS b 29 HIS b 36 HIS C 82 GLN E 97 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 ASN F 345 ASN f 21 HIS ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 HIS G 114 ASN G 115 HIS g 13 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 ASN I 167 ASN i 18 ASN i 52 GLN i 69 HIS J 186 HIS ** j 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 100 ASN ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 ASN ** M 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 GLN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS N 17 HIS N 25 HIS N 28 GLN ** n 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 52 HIS ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 HIS R 137 ASN S 9 GLN ** s 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 91 HIS T 68 GLN U 108 GLN U 114 HIS ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 GLN W 87 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1525 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 139031 Z= 0.347 Angle : 1.080 19.751 205314 Z= 0.536 Chirality : 0.052 0.403 25874 Planarity : 0.009 0.178 12679 Dihedral : 24.557 179.914 59493 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.93 % Favored : 91.66 % Rotamer: Outliers : 2.52 % Allowed : 6.54 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.09), residues: 6345 helix: -1.86 (0.10), residues: 1883 sheet: -1.68 (0.16), residues: 826 loop : -1.60 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP l 49 HIS 0.024 0.004 HIS K 232 PHE 0.046 0.004 PHE H 223 TYR 0.048 0.004 TYR F 92 ARG 0.021 0.002 ARG M 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 325 time to evaluate : 6.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 60 residues processed: 424 average time/residue: 1.2838 time to fit residues: 941.3178 Evaluate side-chains 307 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 5.419 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 2 residues processed: 60 average time/residue: 0.9890 time to fit residues: 116.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 901 optimal weight: 9.9990 chunk 686 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 435 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 915 optimal weight: 9.9990 chunk 969 optimal weight: 5.9990 chunk 478 optimal weight: 20.0000 chunk 867 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 HIS ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN C 23 HIS c 62 HIS ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS G 361 HIS ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** i 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 132 ASN ** M 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN N 106 GLN n 19 GLN O 41 GLN ** o 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN ** s 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 HIS T 166 ASN ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2018 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 139031 Z= 0.355 Angle : 1.062 21.241 205314 Z= 0.533 Chirality : 0.053 0.553 25874 Planarity : 0.008 0.093 12679 Dihedral : 25.016 179.558 59493 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.00 % Favored : 90.53 % Rotamer: Outliers : 3.30 % Allowed : 9.42 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.09), residues: 6345 helix: -2.08 (0.10), residues: 1905 sheet: -1.77 (0.17), residues: 714 loop : -2.04 (0.09), residues: 3726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP K 233 HIS 0.025 0.003 HIS F 273 PHE 0.040 0.004 PHE L 97 TYR 0.068 0.004 TYR P 94 ARG 0.070 0.002 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 327 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 74 residues processed: 470 average time/residue: 1.2116 time to fit residues: 971.2474 Evaluate side-chains 336 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 262 time to evaluate : 6.030 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 74 outliers final: 1 residues processed: 74 average time/residue: 0.9715 time to fit residues: 141.1746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 807 optimal weight: 7.9990 chunk 550 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 721 optimal weight: 5.9990 chunk 400 optimal weight: 30.0000 chunk 827 optimal weight: 2.9990 chunk 670 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 495 optimal weight: 7.9990 chunk 870 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 81 GLN ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** E 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 113 GLN K 79 GLN K 191 ASN ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN o 117 HIS P 15 GLN ** P 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN R 137 ASN ** s 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 157 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2095 moved from start: 0.9442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 139031 Z= 0.269 Angle : 0.890 17.703 205314 Z= 0.449 Chirality : 0.046 0.394 25874 Planarity : 0.006 0.082 12679 Dihedral : 24.779 179.952 59493 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.14 % Favored : 90.43 % Rotamer: Outliers : 1.98 % Allowed : 12.02 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -2.80 (0.09), residues: 6345 helix: -1.73 (0.10), residues: 1883 sheet: -1.56 (0.18), residues: 707 loop : -2.03 (0.09), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP f 60 HIS 0.014 0.002 HIS N 13 PHE 0.027 0.003 PHE F 365 TYR 0.030 0.003 TYR M 89 ARG 0.014 0.001 ARG K 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 296 time to evaluate : 6.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 53 residues processed: 378 average time/residue: 1.2213 time to fit residues: 783.1097 Evaluate side-chains 317 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 6.125 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.9964 time to fit residues: 103.6573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 326 optimal weight: 8.9990 chunk 873 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 569 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 970 optimal weight: 2.9990 chunk 805 optimal weight: 7.9990 chunk 449 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 509 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 4 GLN ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 HIS ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 HIS ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 18 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN K 191 ASN ** K 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 HIS P 182 ASN ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 HIS U 65 ASN W 25 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2263 moved from start: 1.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 139031 Z= 0.282 Angle : 0.907 19.415 205314 Z= 0.456 Chirality : 0.047 0.433 25874 Planarity : 0.007 0.077 12679 Dihedral : 24.885 179.742 59493 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.91 % Favored : 89.66 % Rotamer: Outliers : 2.07 % Allowed : 13.34 % Favored : 84.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.09), residues: 6345 helix: -1.67 (0.11), residues: 1858 sheet: -1.47 (0.18), residues: 695 loop : -2.17 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP f 60 HIS 0.014 0.002 HIS K 138 PHE 0.038 0.003 PHE V 19 TYR 0.031 0.003 TYR Q 112 ARG 0.030 0.001 ARG L 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 295 time to evaluate : 5.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 51 residues processed: 380 average time/residue: 1.3262 time to fit residues: 858.1312 Evaluate side-chains 322 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 271 time to evaluate : 6.084 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 1.0519 time to fit residues: 106.9900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 935 optimal weight: 0.0370 chunk 109 optimal weight: 9.9990 chunk 552 optimal weight: 7.9990 chunk 708 optimal weight: 30.0000 chunk 549 optimal weight: 0.4980 chunk 816 optimal weight: 9.9990 chunk 541 optimal weight: 0.3980 chunk 966 optimal weight: 5.9990 chunk 604 optimal weight: 5.9990 chunk 589 optimal weight: 2.9990 chunk 446 optimal weight: 9.9990 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 GLN a 81 GLN ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 HIS c 49 HIS d 19 ASN E 50 HIS E 205 ASN E 216 HIS ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 57 GLN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 71 HIS g 121 ASN H 32 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 ASN ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 ASN ** j 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN K 232 HIS L 100 ASN L 163 GLN l 28 HIS M 90 GLN ** M 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 58 GLN U 3 HIS U 142 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1993 moved from start: 1.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 139031 Z= 0.166 Angle : 0.702 15.583 205314 Z= 0.356 Chirality : 0.039 0.500 25874 Planarity : 0.005 0.067 12679 Dihedral : 24.485 179.693 59493 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.63 % Favored : 91.98 % Rotamer: Outliers : 0.89 % Allowed : 14.30 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 6345 helix: -1.19 (0.11), residues: 1931 sheet: -1.35 (0.18), residues: 728 loop : -1.88 (0.10), residues: 3686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP T 23 HIS 0.019 0.001 HIS f 17 PHE 0.041 0.002 PHE P 130 TYR 0.032 0.002 TYR P 30 ARG 0.020 0.001 ARG f 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 6.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 16 residues processed: 327 average time/residue: 1.2888 time to fit residues: 719.8071 Evaluate side-chains 272 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 6.103 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.9346 time to fit residues: 36.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 598 optimal weight: 20.0000 chunk 386 optimal weight: 5.9990 chunk 577 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 614 optimal weight: 6.9990 chunk 658 optimal weight: 20.0000 chunk 477 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 759 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 59 ASN K 191 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 152 HIS ** m 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN o 109 ASN P 87 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 HIS s 13 ASN s 122 HIS s 143 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2588 moved from start: 1.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 139031 Z= 0.354 Angle : 1.105 20.751 205314 Z= 0.545 Chirality : 0.053 0.494 25874 Planarity : 0.008 0.171 12679 Dihedral : 25.237 179.629 59493 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 36.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.62 % Favored : 87.88 % Rotamer: Outliers : 1.60 % Allowed : 15.03 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.09), residues: 6345 helix: -1.86 (0.10), residues: 1843 sheet: -1.57 (0.19), residues: 681 loop : -2.34 (0.09), residues: 3821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP f 60 HIS 0.019 0.003 HIS f 17 PHE 0.042 0.004 PHE L 97 TYR 0.083 0.004 TYR F 283 ARG 0.015 0.002 ARG P 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 294 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 43 residues processed: 349 average time/residue: 1.3134 time to fit residues: 776.6941 Evaluate side-chains 309 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 6.218 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 1.0745 time to fit residues: 91.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 879 optimal weight: 3.9990 chunk 926 optimal weight: 2.9990 chunk 844 optimal weight: 0.8980 chunk 900 optimal weight: 30.0000 chunk 925 optimal weight: 1.9990 chunk 542 optimal weight: 0.7980 chunk 392 optimal weight: 2.9990 chunk 707 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 chunk 814 optimal weight: 8.9990 chunk 852 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 81 GLN b 103 GLN b 106 GLN c 28 HIS E 218 HIS ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 35 GLN ** g 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN h 88 ASN ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN M 90 GLN n 4 GLN O 105 GLN o 90 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2217 moved from start: 1.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 139031 Z= 0.177 Angle : 0.744 16.651 205314 Z= 0.376 Chirality : 0.041 0.532 25874 Planarity : 0.005 0.076 12679 Dihedral : 24.725 179.935 59493 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.56 % Favored : 91.05 % Rotamer: Outliers : 0.41 % Allowed : 16.10 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 6345 helix: -1.32 (0.11), residues: 1900 sheet: -1.41 (0.19), residues: 690 loop : -2.08 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP P 200 HIS 0.012 0.001 HIS f 17 PHE 0.026 0.002 PHE P 130 TYR 0.032 0.002 TYR K 55 ARG 0.018 0.001 ARG a 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 291 average time/residue: 1.2272 time to fit residues: 611.5127 Evaluate side-chains 262 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 5.440 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 1.1156 time to fit residues: 27.0532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 897 optimal weight: 30.0000 chunk 591 optimal weight: 20.0000 chunk 952 optimal weight: 8.9990 chunk 581 optimal weight: 3.9990 chunk 451 optimal weight: 0.8980 chunk 662 optimal weight: 4.9990 chunk 999 optimal weight: 8.9990 chunk 919 optimal weight: 0.0570 chunk 795 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 614 optimal weight: 7.9990 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 28 HIS E 205 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS ** R 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 112 GLN ** s 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2372 moved from start: 1.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 139031 Z= 0.211 Angle : 0.791 18.105 205314 Z= 0.397 Chirality : 0.042 0.624 25874 Planarity : 0.006 0.073 12679 Dihedral : 24.741 179.893 59493 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.97 % Favored : 88.64 % Rotamer: Outliers : 0.55 % Allowed : 16.52 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.10), residues: 6345 helix: -1.29 (0.11), residues: 1899 sheet: -1.39 (0.19), residues: 690 loop : -2.17 (0.10), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP U 42 HIS 0.032 0.002 HIS g 88 PHE 0.026 0.002 PHE P 130 TYR 0.039 0.002 TYR I 10 ARG 0.013 0.001 ARG i 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12690 Ramachandran restraints generated. 6345 Oldfield, 0 Emsley, 6345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 6.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 283 average time/residue: 1.3357 time to fit residues: 646.4765 Evaluate side-chains 269 residues out of total 5368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 6.122 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 1.0930 time to fit residues: 39.0775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 487 optimal weight: 1.9990 chunk 632 optimal weight: 8.9990 chunk 847 optimal weight: 0.0030 chunk 243 optimal weight: 20.0000 chunk 733 optimal weight: 0.8980 chunk 117 optimal weight: 50.0000 chunk 221 optimal weight: 10.0000 chunk 796 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 chunk 818 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 3.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 32 GLN c 28 HIS ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** F 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN T 121 HIS ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.257385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.245792 restraints weight = 365852.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.248696 restraints weight = 189762.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.250690 restraints weight = 117472.326| |-----------------------------------------------------------------------------| r_work (final): 0.5065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5065 r_free = 0.5065 target_work(ls_wunit_k1) = 0.250 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5065 r_free = 0.5065 target_work(ls_wunit_k1) = 0.250 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.5065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2383 moved from start: 1.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 139031 Z= 0.189 Angle : 0.745 18.841 205314 Z= 0.374 Chirality : 0.040 0.527 25874 Planarity : 0.005 0.074 12679 Dihedral : 24.681 179.896 59493 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.05 % Favored : 90.56 % Rotamer: Outliers : 0.28 % Allowed : 16.59 % Favored : 83.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 6345 helix: -1.15 (0.11), residues: 1921 sheet: -1.45 (0.19), residues: 698 loop : -2.14 (0.10), residues: 3726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 55 HIS 0.034 0.002 HIS g 88 PHE 0.030 0.002 PHE Q 47 TYR 0.034 0.002 TYR k 53 ARG 0.018 0.001 ARG H 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17023.28 seconds wall clock time: 308 minutes 45.99 seconds (18525.99 seconds total)