Starting phenix.real_space_refine on Fri Dec 8 18:55:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c6j_16452/12_2023/8c6j_16452_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 P 472 5.49 5 Mg 7 5.21 5 S 310 5.16 5 C 64717 2.51 5 N 21824 2.21 5 O 23895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 ASP 39": "OD1" <-> "OD2" Residue "4 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 138": "OD1" <-> "OD2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1233": "OD1" <-> "OD2" Residue "A ASP 1441": "OD1" <-> "OD2" Residue "A TYR 1620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1948": "OD1" <-> "OD2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 652": "OD1" <-> "OD2" Residue "C PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 723": "OD1" <-> "OD2" Residue "CN GLU 66": "OE1" <-> "OE2" Residue "CN GLU 80": "OE1" <-> "OE2" Residue "CN GLU 219": "OE1" <-> "OE2" Residue "F TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 693": "OE1" <-> "OE2" Residue "F TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 718": "OD1" <-> "OD2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G ASP 104": "OD1" <-> "OD2" Residue "H GLU 504": "OE1" <-> "OE2" Residue "H PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 266": "OE1" <-> "OE2" Residue "J PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 491": "OE1" <-> "OE2" Residue "O GLU 190": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 430": "OD1" <-> "OD2" Residue "Z GLU 342": "OE1" <-> "OE2" Residue "h TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 85": "OE1" <-> "OE2" Residue "o TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 362": "OE1" <-> "OE2" Residue "o PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 482": "OD1" <-> "OD2" Residue "y ASP 207": "OD1" <-> "OD2" Residue "z ASP 103": "OD1" <-> "OD2" Residue "z GLU 115": "OE1" <-> "OE2" Residue "z GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 111233 Number of models: 1 Model: "" Number of chains: 69 Chain: "2" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 3010 Classifications: {'RNA': 142} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 58, 'rna3p_pyr': 59} Link IDs: {'rna2p': 25, 'rna3p': 116} Chain breaks: 2 Chain: "4" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 636 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "5" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2371 Classifications: {'RNA': 113} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 39, 'rna3p_pyr': 53} Link IDs: {'rna2p': 20, 'rna3p': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "6" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 35} Link IDs: {'rna2p': 20, 'rna3p': 76} Chain: "7" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3130 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain: "8" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "9" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 595 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 128} Link IDs: {'PTRANS': 6, 'TRANS': 137} Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 335 Chain: "A" Number of atoms: 17716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2261, 17716 Classifications: {'peptide': 2261} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 230} Link IDs: {'PCIS': 2, 'PTRANS': 125, 'TRANS': 2133} Chain breaks: 1 Unresolved non-hydrogen bonds: 1085 Unresolved non-hydrogen angles: 1567 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 298 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 12, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 6, 'HIS:plan': 12, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 594 Chain: "B" Number of atoms: 7141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1726, 7141 Classifications: {'peptide': 1726} Incomplete info: {'backbone_only': 1567} Link IDs: {'PTRANS': 79, 'TRANS': 1646} Unresolved non-hydrogen bonds: 6954 Unresolved non-hydrogen angles: 10023 Unresolved non-hydrogen dihedrals: 4435 Unresolved non-hydrogen chiralities: 2101 Planarities with less than four sites: {'GLN:plan1': 83, 'ASP:plan': 89, 'TYR:plan': 61, 'ASN:plan1': 70, 'TRP:plan': 19, 'HIS:plan': 52, 'PHE:plan': 65, 'GLU:plan': 126, 'ARG:plan': 88} Unresolved non-hydrogen planarities: 3357 Chain: "C" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7114 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 54, 'TRANS': 844} Chain: "C3" Number of atoms: 669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 661 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 138} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 182 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 330 Conformer: "B" Number of residues, atoms: 160, 661 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 138} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 908 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 182 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 330 bond proxies already assigned to first conformer: 657 Chain: "CD" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1025 Classifications: {'peptide': 245} Incomplete info: {'backbone_only': 211} Link IDs: {'PTRANS': 15, 'TRANS': 229} Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1327 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 282 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 11, 'GLU:plan': 15, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 396 Chain: "CE" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 322 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 170 Chain: "CF" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 746 Classifications: {'peptide': 185} Incomplete info: {'backbone_only': 177} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 828 Unresolved non-hydrogen angles: 1159 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 398 Chain: "CI" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 283 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 67} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 14, 'ARG:plan': 8, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "CN" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1643 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 21, 'TRANS': 228} Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 130 Chain: "CT" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 414 Classifications: {'peptide': 102} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 185 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1013 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "E" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 511 Classifications: {'RNA': 24} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 10, 'rna3p': 13} Chain: "F" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1088 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain: "G" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 494 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3321 Classifications: {'peptide': 459} Incomplete info: {'backbone_only': 93, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 431 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 207 Chain: "I" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1727 Classifications: {'RNA': 84} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 20, 'rna3p_pur': 13, 'rna3p_pyr': 40} Link IDs: {'rna2p': 31, 'rna3p': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2720 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 42} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "K" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2360 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 270} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1188 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "M" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2327 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "N" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2388 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "O" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 3321 Classifications: {'peptide': 548} Incomplete info: {'backbone_only': 268} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 2 Unresolved non-hydrogen bonds: 1221 Unresolved non-hydrogen angles: 1723 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 335 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 14, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 11, 'PHE:plan': 4, 'GLU:plan': 37, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 601 Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 973 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "R" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 399 Classifications: {'peptide': 76} Incomplete info: {'backbone_only': 47} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 123 Chain: "S" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 3835 Classifications: {'peptide': 635} Incomplete info: {'backbone_only': 345, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 614} Chain breaks: 1 Unresolved non-hydrogen bonds: 1693 Unresolved non-hydrogen angles: 2399 Unresolved non-hydrogen dihedrals: 1155 Unresolved non-hydrogen chiralities: 428 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'TYR:plan': 19, 'ASN:plan1': 12, 'TRP:plan': 9, 'ASP:plan': 19, 'PHE:plan': 20, 'GLU:plan': 48, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 950 Chain: "T" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 4273 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PTRANS': 21, 'TRANS': 667} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1557 Unresolved non-hydrogen angles: 1995 Unresolved non-hydrogen dihedrals: 1319 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 15, 'TYR:plan': 21, 'ASN:plan1': 14, 'TRP:plan': 10, 'ASP:plan': 27, 'PHE:plan': 17, 'GLU:plan': 37, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 984 Chain: "U" Number of atoms: 5548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1330, 5536 Classifications: {'peptide': 1330} Incomplete info: {'backbone_only': 1201} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 69, 'TRANS': 1255} Chain breaks: 3 Unresolved non-hydrogen bonds: 5582 Unresolved non-hydrogen angles: 8011 Unresolved non-hydrogen dihedrals: 3646 Unresolved non-hydrogen chiralities: 1587 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 39, 'PHE:plan': 77, 'GLU:plan': 100, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2939 Conformer: "B" Number of residues, atoms: 1330, 5536 Classifications: {'peptide': 1330} Incomplete info: {'backbone_only': 1201} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 69, 'TRANS': 1255} Chain breaks: 3 Unresolved non-hydrogen bonds: 5582 Unresolved non-hydrogen angles: 8011 Unresolved non-hydrogen dihedrals: 3646 Unresolved non-hydrogen chiralities: 1587 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 39, 'PHE:plan': 77, 'GLU:plan': 100, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2939 bond proxies already assigned to first conformer: 5586 Chain: "V" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 4167 Classifications: {'peptide': 934} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 782, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 3379 Unresolved non-hydrogen angles: 4850 Unresolved non-hydrogen dihedrals: 2120 Unresolved non-hydrogen chiralities: 1040 Planarities with less than four sites: {'GLN:plan1': 43, 'ARG:plan': 46, 'TYR:plan': 29, 'ASN:plan1': 23, 'TRP:plan': 5, 'HIS:plan': 13, 'ARG%COO:plan': 1, 'PHE:plan': 29, 'GLU:plan': 67, 'ASP:plan': 49} Unresolved non-hydrogen planarities: 1525 Chain: "W" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 722 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 162} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 708 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 221 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 323 Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 377 Classifications: {'peptide': 92} Incomplete info: {'backbone_only': 84} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 179 Chain: "Z" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 454 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 56} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 146 Chain: "a" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 520 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 161 Chain: "b" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 413 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 136 Chain: "c" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 402 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 102 Chain: "d" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "e" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 393 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "f" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 359 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "g" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 69} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "h" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 1 Chain: "i" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1270 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "j" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 398 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 85} Link IDs: {'PTRANS': 6, 'TRANS': 88} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 Chain: "k" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 340 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 151 Chain: "l" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 329 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 116 Chain: "m" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 395 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 87} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "n" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 341 Classifications: {'peptide': 83} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "o" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3918 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 54} Link IDs: {'PTRANS': 24, 'TRANS': 488} Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 119 Chain: "p" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 327 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 76} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 168 Chain: "q" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 300 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 59} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "r" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 302 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 69} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "s" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 922 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 208} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1353 Unresolved non-hydrogen dihedrals: 609 Unresolved non-hydrogen chiralities: 261 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 10, 'PHE%COO:plan': 1, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 518 Chain: "t" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 581 Classifications: {'peptide': 137} Incomplete info: {'backbone_only': 125} Link IDs: {'PTRANS': 11, 'TRANS': 125} Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 237 Chain: "u" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 550 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 119} Link IDs: {'PTRANS': 10, 'TRANS': 119} Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 712 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "v" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 585 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 126} Link IDs: {'PTRANS': 11, 'TRANS': 126} Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 237 Chain: "w" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 554 Classifications: {'peptide': 131} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 159 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "y" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1423 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 213 Chain: "z" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 606 Classifications: {'peptide': 103} Incomplete info: {'backbone_only': 51} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "6" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' K': 2, ' MG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 63751 SG CYS L 105 188.016 102.969 186.697 1.00 42.60 S ATOM 63845 SG CYS L 117 187.029 102.179 183.079 1.00 41.85 S ATOM 63859 SG CYS L 119 190.156 100.718 184.666 1.00 41.23 S ATOM 63978 SG CYS L 134 189.959 104.476 183.796 1.00 46.72 S ATOM 63720 SG CYS L 101 191.299 101.880 188.076 1.00 40.05 S ATOM 63726 SG CYS L 102 188.912 104.364 190.027 1.00 39.59 S ATOM 63751 SG CYS L 105 188.016 102.969 186.697 1.00 42.60 S ATOM 64001 SG CYS L 137 191.049 105.439 187.179 1.00 39.17 S ATOM 63720 SG CYS L 101 191.299 101.880 188.076 1.00 40.05 S ATOM 63859 SG CYS L 119 190.156 100.718 184.666 1.00 41.23 S ATOM 64011 SG CYS L 139 193.827 101.715 185.172 1.00 47.30 S ATOM 64032 SG CYS L 142 192.556 98.602 186.826 1.00 49.00 S ATOM 65228 SG CYS M 165 191.072 116.359 168.013 1.00 48.55 S ATOM 65294 SG CYS M 173 194.336 115.300 169.741 1.00 55.89 S ATOM 65342 SG CYS M 179 191.163 113.070 170.001 1.00 56.95 S ATOM 64266 SG CYS M 45 161.938 112.929 163.913 1.00 42.39 S ATOM 64289 SG CYS M 48 158.487 114.000 164.716 1.00 40.94 S ATOM 64485 SG CYS M 71 159.109 110.314 164.352 1.00 38.91 S ATOM 64507 SG CYS M 74 159.286 112.501 161.248 1.00 38.18 S ATOM 64095 SG CYS M 24 170.511 102.134 156.464 1.00 50.87 S ATOM 64117 SG CYS M 27 171.938 102.145 160.238 1.00 50.67 S ATOM 64560 SG CYS M 81 169.622 104.046 159.065 1.00 43.96 S ATOM 64582 SG CYS M 84 173.029 104.979 157.716 1.00 43.14 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AASNC3 64 " occ=0.50 ... (6 atoms not shown) pdb=" O BASNC3 64 " occ=0.50 residue: pdb=" N AHISC3 110 " occ=0.50 ... (6 atoms not shown) pdb=" O BHISC3 110 " occ=0.50 residue: pdb=" N AMET U 79 " occ=0.49 ... (6 atoms not shown) pdb=" O BMET U 79 " occ=0.51 residue: pdb=" N AMET U 326 " occ=0.45 ... (6 atoms not shown) pdb=" O BMET U 326 " occ=0.45 residue: pdb=" N TYR U 499 " occ=0.00 ... (2 atoms not shown) pdb=" O TYR U 499 " occ=0.00 residue: pdb=" N HIS U 881 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS U 881 " occ=0.00 residue: pdb=" N GLY U 882 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY U 882 " occ=0.00 residue: pdb=" N GLU U 883 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU U 883 " occ=0.00 Time building chain proxies: 47.68, per 1000 atoms: 0.43 Number of scatterers: 111233 At special positions: 0 Unit cell: (247.8, 341.25, 347.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 310 16.00 P 472 15.00 Mg 7 11.99 O 23895 8.00 N 21824 7.00 C 64717 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: 35.95 Conformation dependent library (CDL) restraints added in 18.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 119 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 117 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 105 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 134 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 137 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 105 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 101 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 102 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 142 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 101 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 139 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 119 " pdb=" ZN M 501 " pdb="ZN ZN M 501 " - pdb=" NE2 HIS M 183 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 165 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 179 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 173 " pdb=" ZN M 502 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 71 " pdb="ZN ZN M 502 " - pdb=" SG CYS M 74 " pdb=" ZN M 503 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 84 " pdb="ZN ZN M 503 " - pdb=" SG CYS M 81 " Number of angles added : 33 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17306 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: 607 helices and 133 sheets defined 52.0% alpha, 13.2% beta 107 base pairs and 198 stacking pairs defined. Time for finding SS restraints: 97.02 Creating SS restraints... Processing helix chain '4' and resid 39 through 56 removed outlier: 3.922A pdb=" N ASP 4 54 " --> pdb=" O VAL 4 50 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 75 removed outlier: 6.614A pdb=" N LYS 4 61 " --> pdb=" O PRO 4 57 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU 4 62 " --> pdb=" O ASP 4 58 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN 4 63 " --> pdb=" O VAL 4 59 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA 4 64 " --> pdb=" O GLU 4 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN 4 65 " --> pdb=" O LYS 4 61 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 155 removed outlier: 3.529A pdb=" N SER 4 153 " --> pdb=" O ASP 4 149 " (cutoff:3.500A) Processing helix chain '4' and resid 157 through 177 removed outlier: 4.053A pdb=" N ARG 4 177 " --> pdb=" O ARG 4 173 " (cutoff:3.500A) Processing helix chain '7' and resid 39 through 44 removed outlier: 3.566A pdb=" N MET 7 43 " --> pdb=" O THR 7 39 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY 7 44 " --> pdb=" O PHE 7 40 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 39 through 44' Processing helix chain '7' and resid 46 through 57 Processing helix chain '7' and resid 62 through 75 removed outlier: 3.792A pdb=" N ILE 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS 7 70 " --> pdb=" O GLN 7 66 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN 7 71 " --> pdb=" O ARG 7 67 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 100 removed outlier: 3.570A pdb=" N PHE 7 92 " --> pdb=" O LYS 7 88 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER 7 93 " --> pdb=" O THR 7 89 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 131 Processing helix chain '7' and resid 145 through 156 Processing helix chain '7' and resid 163 through 174 Processing helix chain '7' and resid 188 through 194 Processing helix chain '7' and resid 196 through 209 removed outlier: 4.908A pdb=" N GLN 7 200 " --> pdb=" O GLY 7 196 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR 7 207 " --> pdb=" O ASP 7 203 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 7 208 " --> pdb=" O VAL 7 204 " (cutoff:3.500A) Proline residue: 7 209 - end of helix Processing helix chain '7' and resid 222 through 233 removed outlier: 3.936A pdb=" N MET 7 228 " --> pdb=" O GLU 7 224 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR 7 229 " --> pdb=" O ILE 7 225 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN 7 230 " --> pdb=" O LEU 7 226 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS 7 231 " --> pdb=" O GLU 7 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE 7 232 " --> pdb=" O MET 7 228 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 7 233 " --> pdb=" O THR 7 229 " (cutoff:3.500A) Processing helix chain '7' and resid 242 through 247 removed outlier: 4.273A pdb=" N THR 7 247 " --> pdb=" O ARG 7 243 " (cutoff:3.500A) Processing helix chain '7' and resid 260 through 272 removed outlier: 3.966A pdb=" N LYS 7 264 " --> pdb=" O ARG 7 260 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE 7 265 " --> pdb=" O GLU 7 261 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP 7 266 " --> pdb=" O GLU 7 262 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 301 removed outlier: 3.803A pdb=" N ASN 7 301 " --> pdb=" O MET 7 297 " (cutoff:3.500A) Processing helix chain '7' and resid 312 through 326 Processing helix chain '7' and resid 334 through 339 removed outlier: 4.428A pdb=" N ALA 7 338 " --> pdb=" O THR 7 334 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG 7 339 " --> pdb=" O ASP 7 335 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 334 through 339' Processing helix chain '7' and resid 357 through 368 removed outlier: 4.010A pdb=" N TYR 7 361 " --> pdb=" O ASN 7 357 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER 7 368 " --> pdb=" O ARG 7 364 " (cutoff:3.500A) Processing helix chain '7' and resid 382 through 397 removed outlier: 4.981A pdb=" N ARG 7 387 " --> pdb=" O ASN 7 383 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE 7 388 " --> pdb=" O ASP 7 384 " (cutoff:3.500A) Processing helix chain '7' and resid 405 through 410 removed outlier: 4.100A pdb=" N ALA 7 408 " --> pdb=" O MET 7 405 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP 7 409 " --> pdb=" O ASN 7 406 " (cutoff:3.500A) Processing helix chain '8' and resid 85 through 97 removed outlier: 3.782A pdb=" N ILE 8 89 " --> pdb=" O THR 8 85 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU 8 95 " --> pdb=" O ASP 8 91 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR 8 96 " --> pdb=" O LYS 8 92 " (cutoff:3.500A) Processing helix chain '8' and resid 123 through 134 Processing helix chain '9' and resid 53 through 68 removed outlier: 3.599A pdb=" N MET 9 57 " --> pdb=" O HIS 9 53 " (cutoff:3.500A) Processing helix chain '9' and resid 73 through 78 removed outlier: 4.552A pdb=" N TRP 9 77 " --> pdb=" O ASP 9 73 " (cutoff:3.500A) Proline residue: 9 78 - end of helix No H-bonds generated for 'chain '9' and resid 73 through 78' Processing helix chain '9' and resid 106 through 114 removed outlier: 4.914A pdb=" N LYS 9 114 " --> pdb=" O VAL 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 115 through 141 Processing helix chain 'A' and resid 26 through 46 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.286A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 93 removed outlier: 4.105A pdb=" N ARG A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N HIS A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.512A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 180 through 185 removed outlier: 6.208A pdb=" N ASP A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 298 through 303 removed outlier: 6.076A pdb=" N ILE A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 395 through 407 removed outlier: 4.477A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.490A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.742A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.537A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 Processing helix chain 'A' and resid 531 through 539 Processing helix chain 'A' and resid 541 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 590 through 596 removed outlier: 4.803A pdb=" N TYR A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.603A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.526A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 673 through 697 removed outlier: 5.165A pdb=" N GLU A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 797 Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 851 removed outlier: 3.947A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 874 Proline residue: A 874 - end of helix Processing helix chain 'A' and resid 875 through 888 Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.644A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.927A pdb=" N ILE A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.658A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 removed outlier: 4.557A pdb=" N VAL A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.950A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1118 Proline residue: A1118 - end of helix Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.282A pdb=" N GLY A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A1128 " --> pdb=" O ASN A1124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1128' Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.507A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Proline residue: A1162 - end of helix Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 4.925A pdb=" N PHE A1174 " --> pdb=" O TRP A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1252 removed outlier: 4.636A pdb=" N GLY A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 removed outlier: 3.559A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1275 " --> pdb=" O MET A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 4.069A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN A1282 " --> pdb=" O VAL A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1282' Processing helix chain 'A' and resid 1283 through 1304 removed outlier: 4.418A pdb=" N ASN A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1312 removed outlier: 3.842A pdb=" N PHE A1311 " --> pdb=" O MET A1307 " (cutoff:3.500A) Proline residue: A1312 - end of helix No H-bonds generated for 'chain 'A' and resid 1307 through 1312' Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.987A pdb=" N GLN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 4.158A pdb=" N TYR A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A1372 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN A1373 " --> pdb=" O TYR A1369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1367 through 1373' Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 4.031A pdb=" N LEU A1408 " --> pdb=" O THR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 4.081A pdb=" N LEU A1422 " --> pdb=" O ARG A1418 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A1423 " --> pdb=" O ILE A1419 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A1424 " --> pdb=" O ASN A1420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1418 through 1424' Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 5.128A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 4.697A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A1446 " --> pdb=" O PHE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 4.261A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1489 removed outlier: 4.299A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A1488 " --> pdb=" O ILE A1484 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1519 through 1539 removed outlier: 4.570A pdb=" N SER A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A1525 " --> pdb=" O ALA A1521 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A1527 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A1529 " --> pdb=" O GLY A1525 " (cutoff:3.500A) Proline residue: A1530 - end of helix Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1580 through 1605 removed outlier: 3.509A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA A1603 " --> pdb=" O GLN A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1622 removed outlier: 4.132A pdb=" N SER A1619 " --> pdb=" O HIS A1615 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A1620 " --> pdb=" O PRO A1616 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N MET A1622 " --> pdb=" O LYS A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1690 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 4.815A pdb=" N ALA A1736 " --> pdb=" O LYS A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1767 through 1773 removed outlier: 4.718A pdb=" N LEU A1771 " --> pdb=" O ASN A1767 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE A1772 " --> pdb=" O TYR A1768 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1773 " --> pdb=" O GLY A1769 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1767 through 1773' Processing helix chain 'A' and resid 1823 through 1828 removed outlier: 4.430A pdb=" N TRP A1827 " --> pdb=" O HIS A1823 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A1828 " --> pdb=" O THR A1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1823 through 1828' Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 4.245A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) Proline residue: A1853 - end of helix Processing helix chain 'A' and resid 1865 through 1877 removed outlier: 4.098A pdb=" N LEU A1869 " --> pdb=" O ARG A1865 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP A1870 " --> pdb=" O LYS A1866 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1892 through 1899 removed outlier: 3.922A pdb=" N CYS A1896 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1897 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A1899 " --> pdb=" O ALA A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1909 Processing helix chain 'A' and resid 1922 through 1927 removed outlier: 4.325A pdb=" N THR A1926 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1947 through 1956 Proline residue: A1956 - end of helix Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.607A pdb=" N GLN A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'A' and resid 2072 through 2090 removed outlier: 3.509A pdb=" N ARG A2076 " --> pdb=" O GLU A2072 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A2088 " --> pdb=" O HIS A2084 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A2089 " --> pdb=" O LEU A2085 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2118 Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.522A pdb=" N LYS A2170 " --> pdb=" O HIS A2166 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU A2171 " --> pdb=" O GLU A2167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2166 through 2171' Processing helix chain 'A' and resid 2189 through 2204 Proline residue: A2204 - end of helix Processing helix chain 'A' and resid 2231 through 2241 removed outlier: 3.562A pdb=" N GLN A2240 " --> pdb=" O GLU A2236 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2257 removed outlier: 4.784A pdb=" N TYR A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A2257 " --> pdb=" O PRO A2253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2252 through 2257' Processing helix chain 'A' and resid 2284 through 2289 removed outlier: 3.653A pdb=" N HIS A2288 " --> pdb=" O MET A2284 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A2289 " --> pdb=" O GLY A2285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2284 through 2289' Processing helix chain 'A' and resid 2306 through 2311 Proline residue: A2311 - end of helix Processing helix chain 'A' and resid 2322 through 2328 removed outlier: 4.588A pdb=" N TYR A2326 " --> pdb=" O GLU A2322 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A2327 " --> pdb=" O GLY A2323 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A2328 " --> pdb=" O GLU A2324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2322 through 2328' Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.922A pdb=" N ALA A 201 " --> pdb=" O ASP A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.783A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 removed outlier: 4.192A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY B 474 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 4.486A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 3.754A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.600A pdb=" N GLU B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 600 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.531A pdb=" N ASP B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.567A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 696 through 716 removed outlier: 3.563A pdb=" N ASN B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.148A pdb=" N GLY B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 754 Processing helix chain 'B' and resid 760 through 769 removed outlier: 4.251A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N CYS B 769 " --> pdb=" O GLU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 781 removed outlier: 4.627A pdb=" N ASP B 776 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Proline residue: B 779 - end of helix Processing helix chain 'B' and resid 790 through 804 removed outlier: 3.662A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 819 removed outlier: 4.639A pdb=" N ALA B 816 " --> pdb=" O THR B 812 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 4.007A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA B 856 " --> pdb=" O MET B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 885 removed outlier: 5.173A pdb=" N GLN B 877 " --> pdb=" O HIS B 873 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR B 878 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 908 removed outlier: 4.107A pdb=" N LYS B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Proline residue: B 898 - end of helix Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.889A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 923 " --> pdb=" O TRP B 919 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 933 Proline residue: B 933 - end of helix Processing helix chain 'B' and resid 939 through 947 Proline residue: B 947 - end of helix Processing helix chain 'B' and resid 949 through 968 Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1026 removed outlier: 3.907A pdb=" N SER B1021 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER B1022 " --> pdb=" O PHE B1018 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU B1023 " --> pdb=" O SER B1019 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B1024 " --> pdb=" O LEU B1020 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASN B1026 " --> pdb=" O SER B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1044 removed outlier: 3.842A pdb=" N LYS B1034 " --> pdb=" O ARG B1030 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU B1035 " --> pdb=" O GLU B1031 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLU B1036 " --> pdb=" O GLU B1032 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B1042 " --> pdb=" O GLN B1038 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B1043 " --> pdb=" O LYS B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1074 through 1103 removed outlier: 3.652A pdb=" N GLY B1089 " --> pdb=" O THR B1085 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 removed outlier: 3.703A pdb=" N LYS B1110 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1133 removed outlier: 4.850A pdb=" N GLN B1131 " --> pdb=" O CYS B1127 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B1132 " --> pdb=" O PRO B1128 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG B1133 " --> pdb=" O LEU B1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1127 through 1133' Processing helix chain 'B' and resid 1136 through 1147 removed outlier: 3.576A pdb=" N LYS B1146 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B1147 " --> pdb=" O ILE B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1157 removed outlier: 4.351A pdb=" N LEU B1153 " --> pdb=" O PRO B1149 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR B1154 " --> pdb=" O PHE B1150 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B1156 " --> pdb=" O ARG B1152 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN B1157 " --> pdb=" O LEU B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1149 through 1157' Processing helix chain 'B' and resid 1158 through 1166 Processing helix chain 'B' and resid 1167 through 1181 removed outlier: 3.850A pdb=" N GLY B1171 " --> pdb=" O MET B1167 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR B1173 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1322 removed outlier: 3.657A pdb=" N GLU B1318 " --> pdb=" O ASN B1314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B1319 " --> pdb=" O SER B1315 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1340 removed outlier: 4.361A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1372 removed outlier: 4.311A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1360 " --> pdb=" O LYS B1356 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B1372 " --> pdb=" O LEU B1368 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 Processing helix chain 'B' and resid 1411 through 1422 Processing helix chain 'B' and resid 1428 through 1440 removed outlier: 4.507A pdb=" N ARG B1438 " --> pdb=" O ILE B1434 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP B1439 " --> pdb=" O LEU B1435 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B1440 " --> pdb=" O SER B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1442 through 1448 removed outlier: 3.970A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE B1448 " --> pdb=" O ASN B1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.508A pdb=" N LEU B1467 " --> pdb=" O ASN B1463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B1480 " --> pdb=" O TYR B1476 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1505 removed outlier: 3.823A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1507 through 1512 removed outlier: 5.827A pdb=" N PHE B1512 " --> pdb=" O ALA B1508 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1553 removed outlier: 5.001A pdb=" N LYS B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Proline residue: B1545 - end of helix Processing helix chain 'B' and resid 1565 through 1584 removed outlier: 3.660A pdb=" N THR B1569 " --> pdb=" O SER B1565 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B1584 " --> pdb=" O CYS B1580 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1605 removed outlier: 3.623A pdb=" N LEU B1597 " --> pdb=" O THR B1593 " (cutoff:3.500A) Proline residue: B1599 - end of helix removed outlier: 3.811A pdb=" N GLU B1602 " --> pdb=" O ILE B1598 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B1603 " --> pdb=" O PRO B1599 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1604 " --> pdb=" O TYR B1600 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER B1605 " --> pdb=" O LEU B1601 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1616 removed outlier: 3.593A pdb=" N ASN B1615 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1639 Processing helix chain 'B' and resid 1647 through 1654 removed outlier: 3.787A pdb=" N CYS B1651 " --> pdb=" O SER B1647 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TRP B1652 " --> pdb=" O ARG B1648 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY B1653 " --> pdb=" O SER B1649 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B1654 " --> pdb=" O LEU B1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1647 through 1654' Processing helix chain 'B' and resid 1680 through 1692 removed outlier: 4.338A pdb=" N ALA B1691 " --> pdb=" O MET B1687 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN B1692 " --> pdb=" O VAL B1688 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1720 removed outlier: 3.610A pdb=" N LYS B1711 " --> pdb=" O GLN B1707 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B1712 " --> pdb=" O GLY B1708 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B1713 " --> pdb=" O SER B1709 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B1720 " --> pdb=" O LYS B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1732 removed outlier: 3.879A pdb=" N CYS B1731 " --> pdb=" O HIS B1727 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1759 removed outlier: 4.127A pdb=" N TRP B1757 " --> pdb=" O ASP B1753 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B1758 " --> pdb=" O TYR B1754 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE B1759 " --> pdb=" O LEU B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1760 through 1767 removed outlier: 3.890A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B1766 " --> pdb=" O ARG B1762 " (cutoff:3.500A) Processing helix chain 'B' and resid 1777 through 1800 Processing helix chain 'B' and resid 1813 through 1823 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1852 removed outlier: 3.810A pdb=" N GLU B1847 " --> pdb=" O ARG B1843 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B1852 " --> pdb=" O ILE B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1863 through 1875 removed outlier: 3.994A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B1874 " --> pdb=" O GLN B1870 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1901 Processing helix chain 'B' and resid 1905 through 1934 removed outlier: 3.885A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1952 removed outlier: 3.950A pdb=" N ALA B1939 " --> pdb=" O TRP B1935 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B1951 " --> pdb=" O GLN B1947 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1963 removed outlier: 4.651A pdb=" N GLN B1962 " --> pdb=" O SER B1958 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU B1963 " --> pdb=" O TYR B1959 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1958 through 1963' Processing helix chain 'B' and resid 1967 through 1978 Processing helix chain 'B' and resid 1981 through 1988 removed outlier: 3.670A pdb=" N ILE B1985 " --> pdb=" O SER B1981 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B1988 " --> pdb=" O ASP B1984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1998 removed outlier: 4.657A pdb=" N GLN B1998 " --> pdb=" O ASN B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2014 removed outlier: 3.884A pdb=" N ASP B2006 " --> pdb=" O SER B2002 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1313 removed outlier: 3.707A pdb=" N LEU B1312 " --> pdb=" O VAL B1309 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B1313 " --> pdb=" O SER B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 1211 through 1216 removed outlier: 3.665A pdb=" N GLY B1216 " --> pdb=" O ASP B1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1211 through 1216' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.983A pdb=" N SER C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Proline residue: C 155 - end of helix Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 211 through 223 removed outlier: 3.796A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.349A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.538A pdb=" N PHE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.547A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TRP C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 4.628A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.659A pdb=" N LYS C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 438 Processing helix chain 'C' and resid 440 through 452 removed outlier: 4.891A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 460 through 468 removed outlier: 4.853A pdb=" N ALA C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 removed outlier: 4.851A pdb=" N ILE C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 555 through 560' Processing helix chain 'C' and resid 599 through 615 Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 633 through 646 Processing helix chain 'C' and resid 693 through 703 removed outlier: 3.800A pdb=" N ALA C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 722 removed outlier: 4.558A pdb=" N LEU C 714 " --> pdb=" O ASN C 710 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 732 removed outlier: 3.800A pdb=" N ILE C 732 " --> pdb=" O ALA C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 775 removed outlier: 4.913A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 824 removed outlier: 3.685A pdb=" N ILE C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Proline residue: C 810 - end of helix removed outlier: 4.244A pdb=" N THR C 824 " --> pdb=" O PHE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 854 removed outlier: 3.563A pdb=" N VAL C 843 " --> pdb=" O PRO C 839 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 892 removed outlier: 4.374A pdb=" N PHE C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 883 " --> pdb=" O ASP C 879 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 885 " --> pdb=" O PHE C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.676A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) Processing helix chain 'C3' and resid 17 through 22 Proline residue: C3 22 - end of helix Processing helix chain 'C3' and resid 23 through 35 Processing helix chain 'C3' and resid 124 through 134 Processing helix chain 'CD' and resid 154 through 168 removed outlier: 3.872A pdb=" N GLUCD 158 " --> pdb=" O SERCD 154 " (cutoff:3.500A) Processing helix chain 'CD' and resid 182 through 187 removed outlier: 3.694A pdb=" N METCD 186 " --> pdb=" O SERCD 182 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYSCD 187 " --> pdb=" O PHECD 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 182 through 187' Processing helix chain 'CD' and resid 189 through 200 Processing helix chain 'CD' and resid 205 through 218 Proline residue: CD 213 - end of helix removed outlier: 3.625A pdb=" N GLYCD 218 " --> pdb=" O THRCD 214 " (cutoff:3.500A) Processing helix chain 'CD' and resid 230 through 250 removed outlier: 3.664A pdb=" N VALCD 234 " --> pdb=" O GLYCD 230 " (cutoff:3.500A) Proline residue: CD 238 - end of helix Processing helix chain 'CD' and resid 266 through 288 removed outlier: 3.683A pdb=" N SERCD 288 " --> pdb=" O LEUCD 284 " (cutoff:3.500A) Processing helix chain 'CD' and resid 302 through 313 removed outlier: 3.624A pdb=" N HISCD 312 " --> pdb=" O GLUCD 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLYCD 313 " --> pdb=" O THRCD 309 " (cutoff:3.500A) Processing helix chain 'CD' and resid 320 through 331 Processing helix chain 'CD' and resid 345 through 353 Processing helix chain 'CD' and resid 354 through 365 removed outlier: 3.729A pdb=" N TYRCD 364 " --> pdb=" O THRCD 360 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHECD 365 " --> pdb=" O ILECD 361 " (cutoff:3.500A) Processing helix chain 'CD' and resid 379 through 390 Processing helix chain 'CE' and resid 18 through 27 Processing helix chain 'CE' and resid 56 through 67 Processing helix chain 'CF' and resid 54 through 65 removed outlier: 4.804A pdb=" N VALCF 65 " --> pdb=" O LYSCF 61 " (cutoff:3.500A) Processing helix chain 'CF' and resid 70 through 118 removed outlier: 4.656A pdb=" N LYSCF 74 " --> pdb=" O LEUCF 70 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALACF 75 " --> pdb=" O ASNCF 71 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYSCF 76 " --> pdb=" O ASPCF 72 " (cutoff:3.500A) Processing helix chain 'CF' and resid 174 through 197 Processing helix chain 'CF' and resid 222 through 235 Processing helix chain 'CF' and resid 238 through 245 removed outlier: 4.200A pdb=" N ARGCF 242 " --> pdb=" O PHECF 238 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SERCF 243 " --> pdb=" O SERCF 239 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALACF 244 " --> pdb=" O GLUCF 240 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLYCF 245 " --> pdb=" O LEUCF 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 238 through 245' Processing helix chain 'CF' and resid 263 through 271 Processing helix chain 'CF' and resid 308 through 316 Processing helix chain 'CI' and resid 168 through 199 Proline residue: CI 172 - end of helix Processing helix chain 'CI' and resid 247 through 284 removed outlier: 3.693A pdb=" N SERCI 269 " --> pdb=" O GLNCI 265 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLUCI 270 " --> pdb=" O LYSCI 266 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THRCI 271 " --> pdb=" O TYRCI 267 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEUCI 272 " --> pdb=" O ALACI 268 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLNCI 273 " --> pdb=" O SERCI 269 " (cutoff:3.500A) Processing helix chain 'CN' and resid 66 through 122 removed outlier: 3.730A pdb=" N ILECN 121 " --> pdb=" O LYSCN 117 " (cutoff:3.500A) Processing helix chain 'CN' and resid 210 through 218 removed outlier: 5.334A pdb=" N LEUCN 214 " --> pdb=" O ASPCN 210 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THRCN 216 " --> pdb=" O VALCN 212 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N SERCN 218 " --> pdb=" O LEUCN 214 " (cutoff:3.500A) Processing helix chain 'CN' and resid 247 through 254 removed outlier: 3.742A pdb=" N LYSCN 253 " --> pdb=" O GLUCN 249 " (cutoff:3.500A) Processing helix chain 'CT' and resid 13 through 19 removed outlier: 3.680A pdb=" N GLUCT 18 " --> pdb=" O ASPCT 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLUCT 19 " --> pdb=" O SERCT 15 " (cutoff:3.500A) Processing helix chain 'CT' and resid 20 through 42 removed outlier: 3.531A pdb=" N SERCT 24 " --> pdb=" O ASPCT 20 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYSCT 42 " --> pdb=" O GLNCT 38 " (cutoff:3.500A) Processing helix chain 'CT' and resid 48 through 55 Processing helix chain 'CT' and resid 161 through 172 removed outlier: 3.522A pdb=" N GLYCT 172 " --> pdb=" O GLNCT 168 " (cutoff:3.500A) Processing helix chain 'CT' and resid 179 through 208 removed outlier: 3.516A pdb=" N LYSCT 206 " --> pdb=" O GLNCT 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 removed outlier: 4.485A pdb=" N ASN D 41 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 77 through 140 Processing helix chain 'F' and resid 656 through 663 Processing helix chain 'G' and resid 59 through 84 removed outlier: 4.583A pdb=" N MET G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU G 75 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS G 83 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 100 removed outlier: 6.021A pdb=" N THR G 100 " --> pdb=" O LEU G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 173 Processing helix chain 'H' and resid 177 through 189 removed outlier: 3.609A pdb=" N GLU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 209 Proline residue: H 209 - end of helix Processing helix chain 'H' and resid 210 through 226 removed outlier: 6.074A pdb=" N VAL H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 248 Processing helix chain 'H' and resid 249 through 267 Processing helix chain 'H' and resid 270 through 285 removed outlier: 4.096A pdb=" N CYS H 274 " --> pdb=" O HIS H 270 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG H 284 " --> pdb=" O LEU H 280 " (cutoff:3.500A) Proline residue: H 285 - end of helix Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.649A pdb=" N GLU H 299 " --> pdb=" O GLY H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 308 Processing helix chain 'H' and resid 309 through 325 Processing helix chain 'H' and resid 329 through 346 Processing helix chain 'H' and resid 361 through 366 removed outlier: 5.197A pdb=" N PHE H 366 " --> pdb=" O GLU H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 385 removed outlier: 4.314A pdb=" N ASN H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE H 385 " --> pdb=" O VAL H 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 379 through 385' Processing helix chain 'H' and resid 390 through 406 Processing helix chain 'H' and resid 448 through 467 removed outlier: 4.250A pdb=" N LEU H 452 " --> pdb=" O THR H 448 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU H 467 " --> pdb=" O ILE H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 480 removed outlier: 3.762A pdb=" N GLU H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 500 removed outlier: 4.002A pdb=" N THR H 486 " --> pdb=" O PRO H 482 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 487 " --> pdb=" O GLU H 483 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU H 488 " --> pdb=" O SER H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 518 removed outlier: 3.937A pdb=" N GLY H 508 " --> pdb=" O GLU H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 536 Processing helix chain 'H' and resid 540 through 558 Processing helix chain 'H' and resid 562 through 567 removed outlier: 4.647A pdb=" N GLU H 566 " --> pdb=" O TRP H 562 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N CYS H 567 " --> pdb=" O SER H 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 562 through 567' Processing helix chain 'H' and resid 576 through 594 Processing helix chain 'H' and resid 595 through 605 Processing helix chain 'H' and resid 606 through 613 Proline residue: H 610 - end of helix removed outlier: 3.643A pdb=" N GLU H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 606 through 613' Processing helix chain 'H' and resid 620 through 635 Processing helix chain 'H' and resid 637 through 648 removed outlier: 4.192A pdb=" N ASP H 641 " --> pdb=" O GLY H 637 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU H 642 " --> pdb=" O GLY H 638 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 643 " --> pdb=" O LEU H 639 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS H 648 " --> pdb=" O ARG H 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 27 Processing helix chain 'J' and resid 36 through 52 Processing helix chain 'J' and resid 496 through 501 Proline residue: J 501 - end of helix Processing helix chain 'K' and resid 98 through 104 removed outlier: 4.464A pdb=" N ALA K 102 " --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 120 removed outlier: 4.226A pdb=" N LEU K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 120 " --> pdb=" O TYR K 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 115 through 120' Processing helix chain 'K' and resid 136 through 164 removed outlier: 4.214A pdb=" N LYS K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN K 157 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA K 161 " --> pdb=" O GLN K 157 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA K 162 " --> pdb=" O LYS K 158 " (cutoff:3.500A) Proline residue: K 164 - end of helix Processing helix chain 'K' and resid 185 through 190 removed outlier: 4.288A pdb=" N ASN K 189 " --> pdb=" O GLY K 185 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER K 190 " --> pdb=" O VAL K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 190' Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.743A pdb=" N TRP K 245 " --> pdb=" O GLU K 241 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS K 246 " --> pdb=" O GLN K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 270 removed outlier: 4.745A pdb=" N ALA K 270 " --> pdb=" O LYS K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 335 removed outlier: 4.427A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.536A pdb=" N PHE K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY K 59 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 35 removed outlier: 3.723A pdb=" N ILE L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 65 removed outlier: 4.299A pdb=" N LEU L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP L 47 " --> pdb=" O VAL L 43 " (cutoff:3.500A) Proline residue: L 48 - end of helix Processing helix chain 'L' and resid 71 through 82 Processing helix chain 'L' and resid 85 through 95 removed outlier: 3.786A pdb=" N LYS L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN L 95 " --> pdb=" O LYS L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 removed outlier: 4.293A pdb=" N ILE L 106 " --> pdb=" O CYS L 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 102 through 108' Processing helix chain 'L' and resid 117 through 122 removed outlier: 3.967A pdb=" N VAL L 121 " --> pdb=" O CYS L 117 " (cutoff:3.500A) Proline residue: L 122 - end of helix No H-bonds generated for 'chain 'L' and resid 117 through 122' Processing helix chain 'M' and resid 24 through 29 removed outlier: 3.809A pdb=" N LEU M 28 " --> pdb=" O CYS M 24 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY M 29 " --> pdb=" O GLN M 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 29' Processing helix chain 'M' and resid 71 through 79 Processing helix chain 'M' and resid 93 through 102 Processing helix chain 'M' and resid 111 through 129 removed outlier: 4.136A pdb=" N SER M 128 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP M 129 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 141 removed outlier: 4.424A pdb=" N LYS M 139 " --> pdb=" O GLY M 135 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA M 140 " --> pdb=" O MET M 136 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR M 141 " --> pdb=" O LEU M 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 135 through 141' Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 156 through 161 removed outlier: 4.715A pdb=" N ASN M 160 " --> pdb=" O TYR M 156 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 156 through 161' Processing helix chain 'M' and resid 165 through 171 Processing helix chain 'M' and resid 197 through 204 Processing helix chain 'M' and resid 207 through 220 removed outlier: 3.550A pdb=" N THR M 219 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET M 220 " --> pdb=" O ARG M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 253 removed outlier: 3.781A pdb=" N LEU M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 288 Processing helix chain 'O' and resid 12 through 26 Processing helix chain 'O' and resid 30 through 39 removed outlier: 3.732A pdb=" N HIS O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 Processing helix chain 'O' and resid 64 through 79 removed outlier: 3.535A pdb=" N LYS O 76 " --> pdb=" O LEU O 72 " (cutoff:3.500A) Proline residue: O 79 - end of helix Processing helix chain 'O' and resid 81 through 90 Proline residue: O 87 - end of helix Processing helix chain 'O' and resid 92 through 109 Processing helix chain 'O' and resid 131 through 136 removed outlier: 4.202A pdb=" N LYS O 135 " --> pdb=" O ASN O 131 " (cutoff:3.500A) Proline residue: O 136 - end of helix No H-bonds generated for 'chain 'O' and resid 131 through 136' Processing helix chain 'O' and resid 145 through 161 Processing helix chain 'O' and resid 164 through 195 Processing helix chain 'O' and resid 209 through 214 removed outlier: 3.979A pdb=" N GLU O 213 " --> pdb=" O ASP O 209 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE O 214 " --> pdb=" O TYR O 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 209 through 214' Processing helix chain 'O' and resid 243 through 249 removed outlier: 3.609A pdb=" N LEU O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 274 Processing helix chain 'O' and resid 275 through 283 removed outlier: 3.744A pdb=" N GLN O 281 " --> pdb=" O SER O 277 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR O 282 " --> pdb=" O ALA O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 514 through 537 removed outlier: 4.539A pdb=" N MET O 537 " --> pdb=" O GLU O 533 " (cutoff:3.500A) Processing helix chain 'O' and resid 538 through 544 Processing helix chain 'O' and resid 552 through 557 removed outlier: 5.339A pdb=" N ARG O 557 " --> pdb=" O GLU O 553 " (cutoff:3.500A) Processing helix chain 'O' and resid 566 through 590 Processing helix chain 'O' and resid 608 through 620 Proline residue: O 620 - end of helix Processing helix chain 'O' and resid 625 through 648 removed outlier: 3.724A pdb=" N LEU O 629 " --> pdb=" O SER O 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 653 through 669 removed outlier: 5.012A pdb=" N LEU O 669 " --> pdb=" O TYR O 665 " (cutoff:3.500A) Processing helix chain 'O' and resid 684 through 726 removed outlier: 5.011A pdb=" N GLY O 723 " --> pdb=" O ILE O 719 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR O 724 " --> pdb=" O LEU O 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 727 through 796 Proline residue: O 764 - end of helix Processing helix chain 'P' and resid 50 through 57 removed outlier: 4.603A pdb=" N ASN P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 57 " --> pdb=" O GLU P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 75 Processing helix chain 'P' and resid 187 through 193 removed outlier: 6.088A pdb=" N ASP P 191 " --> pdb=" O ARG P 187 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL P 192 " --> pdb=" O TRP P 188 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 187 through 193' Processing helix chain 'P' and resid 202 through 210 removed outlier: 4.304A pdb=" N LYS P 206 " --> pdb=" O ASP P 202 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS P 208 " --> pdb=" O GLN P 204 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE P 210 " --> pdb=" O LYS P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'R' and resid 54 through 81 Processing helix chain 'R' and resid 83 through 101 Processing helix chain 'S' and resid 29 through 41 removed outlier: 4.284A pdb=" N GLU S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 78 Processing helix chain 'S' and resid 80 through 95 removed outlier: 4.108A pdb=" N TRP S 84 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 112 Processing helix chain 'S' and resid 114 through 129 removed outlier: 3.635A pdb=" N TRP S 118 " --> pdb=" O ASN S 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU S 125 " --> pdb=" O TYR S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 145 Processing helix chain 'S' and resid 148 through 163 removed outlier: 3.803A pdb=" N TRP S 152 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY S 163 " --> pdb=" O GLU S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 179 removed outlier: 3.992A pdb=" N TRP S 178 " --> pdb=" O ARG S 174 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN S 179 " --> pdb=" O TRP S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 196 removed outlier: 3.708A pdb=" N TYR S 195 " --> pdb=" O PHE S 191 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS S 196 " --> pdb=" O GLU S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 197 through 213 Proline residue: S 213 - end of helix Processing helix chain 'S' and resid 214 through 229 removed outlier: 3.588A pdb=" N ALA S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 246 Processing helix chain 'S' and resid 251 through 266 removed outlier: 3.829A pdb=" N TYR S 255 " --> pdb=" O ASP S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 267 through 282 removed outlier: 3.508A pdb=" N ASP S 280 " --> pdb=" O LYS S 276 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG S 281 " --> pdb=" O TYR S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 288 through 301 Processing helix chain 'S' and resid 303 through 319 Processing helix chain 'S' and resid 329 through 344 Processing helix chain 'S' and resid 345 through 360 removed outlier: 3.761A pdb=" N ASN S 359 " --> pdb=" O ARG S 355 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL S 360 " --> pdb=" O ALA S 356 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 386 removed outlier: 4.472A pdb=" N ARG S 371 " --> pdb=" O ARG S 367 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR S 372 " --> pdb=" O HIS S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 389 through 405 Proline residue: S 405 - end of helix Processing helix chain 'S' and resid 411 through 426 removed outlier: 3.988A pdb=" N TRP S 415 " --> pdb=" O PHE S 411 " (cutoff:3.500A) Processing helix chain 'S' and resid 427 through 442 Processing helix chain 'S' and resid 444 through 459 Processing helix chain 'S' and resid 460 through 473 Processing helix chain 'S' and resid 479 through 493 removed outlier: 4.184A pdb=" N ILE S 483 " --> pdb=" O CYS S 479 " (cutoff:3.500A) Processing helix chain 'S' and resid 494 through 508 Processing helix chain 'S' and resid 513 through 529 removed outlier: 3.909A pdb=" N LEU S 517 " --> pdb=" O MET S 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 530 through 545 Processing helix chain 'S' and resid 547 through 562 removed outlier: 3.529A pdb=" N TRP S 551 " --> pdb=" O HIS S 547 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY S 562 " --> pdb=" O GLU S 558 " (cutoff:3.500A) Processing helix chain 'S' and resid 565 through 585 removed outlier: 5.155A pdb=" N GLU S 585 " --> pdb=" O MET S 581 " (cutoff:3.500A) Processing helix chain 'S' and resid 586 through 604 removed outlier: 3.613A pdb=" N ARG S 590 " --> pdb=" O GLU S 586 " (cutoff:3.500A) Processing helix chain 'S' and resid 606 through 617 removed outlier: 3.539A pdb=" N LEU S 616 " --> pdb=" O ARG S 612 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET S 617 " --> pdb=" O VAL S 613 " (cutoff:3.500A) Processing helix chain 'S' and resid 645 through 653 removed outlier: 3.824A pdb=" N ASN S 651 " --> pdb=" O GLU S 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN S 652 " --> pdb=" O ASP S 648 " (cutoff:3.500A) Proline residue: S 653 - end of helix Processing helix chain 'T' and resid 21 through 32 Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.957A pdb=" N TRP T 38 " --> pdb=" O SER T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 65 Proline residue: T 65 - end of helix Processing helix chain 'T' and resid 67 through 83 removed outlier: 3.885A pdb=" N LYS T 83 " --> pdb=" O ARG T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 106 removed outlier: 3.515A pdb=" N GLU T 100 " --> pdb=" O ASN T 96 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.773A pdb=" N TRP T 113 " --> pdb=" O MET T 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET T 121 " --> pdb=" O CYS T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 141 removed outlier: 4.284A pdb=" N THR T 129 " --> pdb=" O ARG T 125 " (cutoff:3.500A) Proline residue: T 141 - end of helix Processing helix chain 'T' and resid 143 through 160 removed outlier: 4.982A pdb=" N ARG T 147 " --> pdb=" O THR T 143 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE T 148 " --> pdb=" O GLN T 144 " (cutoff:3.500A) Proline residue: T 150 - end of helix removed outlier: 4.273A pdb=" N HIS T 159 " --> pdb=" O PHE T 155 " (cutoff:3.500A) Proline residue: T 160 - end of helix Processing helix chain 'T' and resid 161 through 177 removed outlier: 4.707A pdb=" N ALA T 165 " --> pdb=" O LEU T 161 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG T 167 " --> pdb=" O GLU T 163 " (cutoff:3.500A) Proline residue: T 177 - end of helix Processing helix chain 'T' and resid 179 through 191 removed outlier: 3.681A pdb=" N TYR T 183 " --> pdb=" O SER T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 207 removed outlier: 4.075A pdb=" N ALA T 196 " --> pdb=" O ARG T 192 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN T 205 " --> pdb=" O ALA T 201 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP T 206 " --> pdb=" O THR T 202 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU T 207 " --> pdb=" O VAL T 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 217 through 232 removed outlier: 4.589A pdb=" N TRP T 221 " --> pdb=" O ASN T 217 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 231 " --> pdb=" O LEU T 227 " (cutoff:3.500A) Proline residue: T 232 - end of helix Processing helix chain 'T' and resid 239 through 252 removed outlier: 5.031A pdb=" N THR T 252 " --> pdb=" O LEU T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 254 through 270 removed outlier: 4.142A pdb=" N LEU T 258 " --> pdb=" O GLN T 254 " (cutoff:3.500A) Processing helix chain 'T' and resid 271 through 286 removed outlier: 4.695A pdb=" N ALA T 275 " --> pdb=" O HIS T 271 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 288 through 313 removed outlier: 3.675A pdb=" N GLN T 294 " --> pdb=" O ARG T 290 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET T 306 " --> pdb=" O PHE T 302 " (cutoff:3.500A) Processing helix chain 'T' and resid 322 through 354 Proline residue: T 342 - end of helix Proline residue: T 354 - end of helix Processing helix chain 'T' and resid 356 through 369 removed outlier: 4.203A pdb=" N GLY T 369 " --> pdb=" O ALA T 365 " (cutoff:3.500A) Processing helix chain 'T' and resid 372 through 384 Processing helix chain 'T' and resid 395 through 409 Processing helix chain 'T' and resid 410 through 423 Processing helix chain 'T' and resid 429 through 447 removed outlier: 3.627A pdb=" N ALA T 433 " --> pdb=" O VAL T 429 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER T 434 " --> pdb=" O ASP T 430 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL T 435 " --> pdb=" O ASP T 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 460 Processing helix chain 'T' and resid 476 through 481 removed outlier: 3.858A pdb=" N VAL T 480 " --> pdb=" O VAL T 476 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR T 481 " --> pdb=" O GLN T 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 476 through 481' Processing helix chain 'T' and resid 483 through 497 Processing helix chain 'T' and resid 502 through 514 removed outlier: 3.704A pdb=" N ASP T 508 " --> pdb=" O LYS T 504 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU T 513 " --> pdb=" O ARG T 509 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG T 514 " --> pdb=" O ILE T 510 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 532 removed outlier: 3.730A pdb=" N TYR T 524 " --> pdb=" O ILE T 520 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS T 531 " --> pdb=" O PHE T 527 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS T 532 " --> pdb=" O LEU T 528 " (cutoff:3.500A) Processing helix chain 'T' and resid 533 through 549 removed outlier: 6.305A pdb=" N SER T 537 " --> pdb=" O TYR T 533 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE T 538 " --> pdb=" O PHE T 534 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE T 548 " --> pdb=" O GLY T 544 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS T 549 " --> pdb=" O ILE T 545 " (cutoff:3.500A) Processing helix chain 'T' and resid 550 through 568 removed outlier: 4.074A pdb=" N SER T 554 " --> pdb=" O TRP T 550 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP T 555 " --> pdb=" O PRO T 551 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE T 556 " --> pdb=" O ASN T 552 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 587 removed outlier: 4.351A pdb=" N LEU T 573 " --> pdb=" O GLY T 569 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU T 574 " --> pdb=" O GLY T 570 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG T 575 " --> pdb=" O ARG T 571 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA T 576 " --> pdb=" O LYS T 572 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY T 586 " --> pdb=" O GLN T 582 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS T 587 " --> pdb=" O ALA T 583 " (cutoff:3.500A) Processing helix chain 'T' and resid 591 through 606 removed outlier: 4.691A pdb=" N LEU T 595 " --> pdb=" O TYR T 591 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU T 598 " --> pdb=" O THR T 594 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR T 599 " --> pdb=" O LEU T 595 " (cutoff:3.500A) Processing helix chain 'T' and resid 608 through 623 removed outlier: 3.710A pdb=" N ALA T 612 " --> pdb=" O LEU T 608 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL T 615 " --> pdb=" O HIS T 611 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR T 616 " --> pdb=" O ALA T 612 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU T 617 " --> pdb=" O MET T 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG T 621 " --> pdb=" O GLU T 617 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA T 622 " --> pdb=" O ARG T 618 " (cutoff:3.500A) Processing helix chain 'T' and resid 625 through 643 removed outlier: 4.084A pdb=" N ILE T 634 " --> pdb=" O ASP T 630 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU T 641 " --> pdb=" O LYS T 637 " (cutoff:3.500A) Processing helix chain 'T' and resid 644 through 659 removed outlier: 3.968A pdb=" N THR T 648 " --> pdb=" O GLY T 644 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG T 649 " --> pdb=" O VAL T 645 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY T 650 " --> pdb=" O THR T 646 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE T 651 " --> pdb=" O HIS T 647 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN T 653 " --> pdb=" O ARG T 649 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS T 654 " --> pdb=" O GLY T 650 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE T 656 " --> pdb=" O TYR T 652 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU T 659 " --> pdb=" O ALA T 655 " (cutoff:3.500A) Processing helix chain 'T' and resid 662 through 679 removed outlier: 4.694A pdb=" N GLU T 666 " --> pdb=" O GLU T 662 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU T 669 " --> pdb=" O ARG T 665 " (cutoff:3.500A) Processing helix chain 'T' and resid 680 through 695 removed outlier: 3.661A pdb=" N ILE T 694 " --> pdb=" O PHE T 690 " (cutoff:3.500A) Processing helix chain 'T' and resid 700 through 715 removed outlier: 6.353A pdb=" N TRP T 704 " --> pdb=" O THR T 700 " (cutoff:3.500A) Processing helix chain 'T' and resid 716 through 736 removed outlier: 3.636A pdb=" N ILE T 720 " --> pdb=" O ASN T 716 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN T 735 " --> pdb=" O GLN T 731 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR T 736 " --> pdb=" O ALA T 732 " (cutoff:3.500A) Processing helix chain 'T' and resid 737 through 749 Processing helix chain 'U' and resid 19 through 31 Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.087A pdb=" N ILE U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE U 54 " --> pdb=" O TYR U 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL U 55 " --> pdb=" O GLU U 51 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS U 56 " --> pdb=" O LYS U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 71 removed outlier: 3.515A pdb=" N GLN U 71 " --> pdb=" O LEU U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 81 Processing helix chain 'U' and resid 87 through 105 Processing helix chain 'U' and resid 109 through 116 Proline residue: U 116 - end of helix Processing helix chain 'U' and resid 118 through 132 Processing helix chain 'U' and resid 139 through 157 removed outlier: 3.752A pdb=" N LEU U 157 " --> pdb=" O CYS U 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 170 removed outlier: 3.888A pdb=" N GLN U 165 " --> pdb=" O LEU U 161 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLN U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU U 169 " --> pdb=" O GLN U 165 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 170 " --> pdb=" O VAL U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 176 removed outlier: 4.340A pdb=" N TRP U 175 " --> pdb=" O SER U 171 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET U 176 " --> pdb=" O LEU U 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 171 through 176' Processing helix chain 'U' and resid 179 through 191 Proline residue: U 191 - end of helix Processing helix chain 'U' and resid 192 through 208 removed outlier: 4.244A pdb=" N PHE U 196 " --> pdb=" O LYS U 192 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS U 206 " --> pdb=" O LYS U 202 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP U 208 " --> pdb=" O ASP U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 236 removed outlier: 4.621A pdb=" N LEU U 222 " --> pdb=" O GLU U 218 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER U 223 " --> pdb=" O ARG U 219 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL U 236 " --> pdb=" O VAL U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 264 removed outlier: 3.708A pdb=" N VAL U 247 " --> pdb=" O THR U 243 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU U 264 " --> pdb=" O LEU U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 278 removed outlier: 4.954A pdb=" N TRP U 269 " --> pdb=" O PRO U 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE U 270 " --> pdb=" O THR U 266 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR U 272 " --> pdb=" O ARG U 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE U 273 " --> pdb=" O TRP U 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 279 through 286 Processing helix chain 'U' and resid 287 through 292 removed outlier: 5.587A pdb=" N GLU U 292 " --> pdb=" O LEU U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 311 Processing helix chain 'U' and resid 322 through 344 Processing helix chain 'U' and resid 345 through 354 removed outlier: 5.161A pdb=" N ASP U 350 " --> pdb=" O PRO U 346 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE U 351 " --> pdb=" O GLU U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 355 through 360 Processing helix chain 'U' and resid 361 through 370 Processing helix chain 'U' and resid 373 through 385 Processing helix chain 'U' and resid 399 through 412 Processing helix chain 'U' and resid 416 through 425 removed outlier: 3.669A pdb=" N MET U 424 " --> pdb=" O GLN U 420 " (cutoff:3.500A) Proline residue: U 425 - end of helix Processing helix chain 'U' and resid 429 through 435 removed outlier: 4.225A pdb=" N TRP U 434 " --> pdb=" O GLU U 430 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP U 435 " --> pdb=" O LYS U 431 " (cutoff:3.500A) Processing helix chain 'U' and resid 461 through 493 removed outlier: 3.573A pdb=" N TYR U 479 " --> pdb=" O LEU U 475 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU U 480 " --> pdb=" O GLU U 476 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS U 493 " --> pdb=" O VAL U 489 " (cutoff:3.500A) Processing helix chain 'U' and resid 546 through 556 removed outlier: 4.052A pdb=" N LEU U 556 " --> pdb=" O GLU U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 582 through 588 Processing helix chain 'U' and resid 630 through 644 Processing helix chain 'U' and resid 648 through 653 removed outlier: 4.050A pdb=" N THR U 652 " --> pdb=" O ASP U 648 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE U 653 " --> pdb=" O VAL U 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 648 through 653' Processing helix chain 'U' and resid 660 through 680 removed outlier: 4.567A pdb=" N ASN U 665 " --> pdb=" O PRO U 661 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE U 666 " --> pdb=" O LYS U 662 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS U 667 " --> pdb=" O GLU U 663 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA U 668 " --> pdb=" O ASN U 664 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP U 680 " --> pdb=" O LEU U 676 " (cutoff:3.500A) Processing helix chain 'U' and resid 684 through 693 removed outlier: 4.571A pdb=" N ASP U 689 " --> pdb=" O ASP U 685 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE U 690 " --> pdb=" O TRP U 686 " (cutoff:3.500A) Processing helix chain 'U' and resid 720 through 729 removed outlier: 3.960A pdb=" N PHE U 728 " --> pdb=" O LEU U 724 " (cutoff:3.500A) Proline residue: U 729 - end of helix Processing helix chain 'U' and resid 739 through 744 removed outlier: 3.525A pdb=" N GLN U 743 " --> pdb=" O ASP U 739 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE U 744 " --> pdb=" O PRO U 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 739 through 744' Processing helix chain 'U' and resid 803 through 816 removed outlier: 3.508A pdb=" N GLN U 815 " --> pdb=" O ARG U 811 " (cutoff:3.500A) Proline residue: U 816 - end of helix Processing helix chain 'U' and resid 828 through 844 Processing helix chain 'U' and resid 855 through 870 removed outlier: 3.671A pdb=" N LEU U 859 " --> pdb=" O SER U 855 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU U 869 " --> pdb=" O LYS U 865 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP U 870 " --> pdb=" O ILE U 866 " (cutoff:3.500A) Processing helix chain 'U' and resid 872 through 877 removed outlier: 4.004A pdb=" N LEU U 876 " --> pdb=" O ASP U 872 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU U 877 " --> pdb=" O GLU U 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 872 through 877' Processing helix chain 'U' and resid 893 through 920 Processing helix chain 'U' and resid 928 through 952 removed outlier: 4.105A pdb=" N MET U 941 " --> pdb=" O LEU U 937 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER U 942 " --> pdb=" O TYR U 938 " (cutoff:3.500A) Processing helix chain 'U' and resid 960 through 968 removed outlier: 3.507A pdb=" N VAL U 964 " --> pdb=" O ASP U 960 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER U 965 " --> pdb=" O VAL U 961 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE U 968 " --> pdb=" O VAL U 964 " (cutoff:3.500A) Processing helix chain 'U' and resid 970 through 975 Processing helix chain 'U' and resid 986 through 1018 removed outlier: 4.498A pdb=" N ALA U1013 " --> pdb=" O GLU U1009 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER U1014 " --> pdb=" O GLU U1010 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU U1015 " --> pdb=" O PHE U1011 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU U1016 " --> pdb=" O ARG U1012 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG U1018 " --> pdb=" O SER U1014 " (cutoff:3.500A) Processing helix chain 'U' and resid 1019 through 1030 Processing helix chain 'U' and resid 1038 through 1046 Processing helix chain 'U' and resid 1047 through 1053 Processing helix chain 'U' and resid 1063 through 1068 removed outlier: 3.809A pdb=" N ILE U1067 " --> pdb=" O GLU U1063 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU U1068 " --> pdb=" O ALA U1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1063 through 1068' Processing helix chain 'U' and resid 1069 through 1079 removed outlier: 3.573A pdb=" N ILE U1074 " --> pdb=" O ILE U1070 " (cutoff:3.500A) Proline residue: U1075 - end of helix removed outlier: 3.959A pdb=" N LEU U1078 " --> pdb=" O ILE U1074 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN U1079 " --> pdb=" O PRO U1075 " (cutoff:3.500A) Processing helix chain 'U' and resid 1106 through 1113 removed outlier: 3.980A pdb=" N GLN U1110 " --> pdb=" O ASN U1106 " (cutoff:3.500A) Processing helix chain 'U' and resid 1118 through 1127 Processing helix chain 'U' and resid 1140 through 1148 removed outlier: 4.147A pdb=" N LEU U1146 " --> pdb=" O SER U1142 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR U1147 " --> pdb=" O LEU U1143 " (cutoff:3.500A) Processing helix chain 'U' and resid 1157 through 1163 Processing helix chain 'U' and resid 1200 through 1218 Processing helix chain 'U' and resid 1220 through 1225 removed outlier: 3.749A pdb=" N ILE U1224 " --> pdb=" O PRO U1220 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER U1225 " --> pdb=" O ALA U1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1220 through 1225' Processing helix chain 'U' and resid 1230 through 1245 Processing helix chain 'U' and resid 1259 through 1264 removed outlier: 3.806A pdb=" N GLN U1264 " --> pdb=" O VAL U1260 " (cutoff:3.500A) Processing helix chain 'U' and resid 1286 through 1297 removed outlier: 3.535A pdb=" N ARG U1296 " --> pdb=" O VAL U1292 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA U1297 " --> pdb=" O ALA U1293 " (cutoff:3.500A) Processing helix chain 'U' and resid 1306 through 1313 removed outlier: 4.144A pdb=" N CYS U1313 " --> pdb=" O LEU U1309 " (cutoff:3.500A) Processing helix chain 'U' and resid 1316 through 1325 removed outlier: 3.947A pdb=" N GLN U1322 " --> pdb=" O PRO U1318 " (cutoff:3.500A) Processing helix chain 'U' and resid 1357 through 1376 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 46 through 61 removed outlier: 3.738A pdb=" N THR V 61 " --> pdb=" O ALA V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 74 Processing helix chain 'V' and resid 78 through 93 Processing helix chain 'V' and resid 110 through 120 Proline residue: V 120 - end of helix Processing helix chain 'V' and resid 126 through 135 removed outlier: 3.619A pdb=" N VAL V 130 " --> pdb=" O ASP V 126 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 153 removed outlier: 3.888A pdb=" N LYS V 140 " --> pdb=" O GLU V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 395 through 409 Processing helix chain 'V' and resid 430 through 435 removed outlier: 5.388A pdb=" N ASP V 434 " --> pdb=" O ASP V 430 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU V 435 " --> pdb=" O ASP V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 451 through 460 removed outlier: 4.260A pdb=" N GLN V 455 " --> pdb=" O GLY V 451 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET V 457 " --> pdb=" O THR V 453 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP V 458 " --> pdb=" O LYS V 454 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET V 459 " --> pdb=" O GLN V 455 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER V 460 " --> pdb=" O SER V 456 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 501 Processing helix chain 'V' and resid 536 through 544 removed outlier: 4.030A pdb=" N GLY V 544 " --> pdb=" O LYS V 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 557 through 565 removed outlier: 3.893A pdb=" N GLU V 563 " --> pdb=" O LEU V 559 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER V 564 " --> pdb=" O GLU V 560 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU V 565 " --> pdb=" O GLN V 561 " (cutoff:3.500A) Processing helix chain 'V' and resid 570 through 582 removed outlier: 4.577A pdb=" N GLN V 582 " --> pdb=" O VAL V 578 " (cutoff:3.500A) Processing helix chain 'V' and resid 595 through 606 Processing helix chain 'V' and resid 619 through 635 Processing helix chain 'V' and resid 662 through 674 removed outlier: 3.701A pdb=" N ILE V 672 " --> pdb=" O ARG V 668 " (cutoff:3.500A) Proline residue: V 674 - end of helix Processing helix chain 'V' and resid 691 through 708 removed outlier: 3.516A pdb=" N GLN V 706 " --> pdb=" O LYS V 702 " (cutoff:3.500A) Processing helix chain 'V' and resid 721 through 730 removed outlier: 3.792A pdb=" N TYR V 730 " --> pdb=" O SER V 726 " (cutoff:3.500A) Processing helix chain 'V' and resid 755 through 770 removed outlier: 3.526A pdb=" N LEU V 761 " --> pdb=" O LEU V 757 " (cutoff:3.500A) Processing helix chain 'V' and resid 782 through 801 removed outlier: 3.828A pdb=" N LEU V 800 " --> pdb=" O ARG V 796 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY V 801 " --> pdb=" O MET V 797 " (cutoff:3.500A) Processing helix chain 'V' and resid 817 through 827 removed outlier: 4.172A pdb=" N ILE V 824 " --> pdb=" O MET V 820 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE V 825 " --> pdb=" O GLN V 821 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP V 826 " --> pdb=" O THR V 822 " (cutoff:3.500A) Proline residue: V 827 - end of helix Processing helix chain 'V' and resid 839 through 844 removed outlier: 4.407A pdb=" N GLU V 843 " --> pdb=" O THR V 839 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR V 844 " --> pdb=" O ASN V 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 839 through 844' Processing helix chain 'V' and resid 880 through 893 removed outlier: 4.041A pdb=" N ALA V 891 " --> pdb=" O ARG V 887 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY V 892 " --> pdb=" O ALA V 888 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG V 893 " --> pdb=" O GLY V 889 " (cutoff:3.500A) Processing helix chain 'V' and resid 904 through 910 removed outlier: 3.562A pdb=" N ARG V 909 " --> pdb=" O GLU V 905 " (cutoff:3.500A) Processing helix chain 'V' and resid 918 through 923 removed outlier: 3.955A pdb=" N ARG V 922 " --> pdb=" O PRO V 918 " (cutoff:3.500A) Processing helix chain 'V' and resid 925 through 936 Processing helix chain 'V' and resid 950 through 965 removed outlier: 5.007A pdb=" N GLY V 965 " --> pdb=" O LEU V 961 " (cutoff:3.500A) Processing helix chain 'V' and resid 976 through 984 Proline residue: V 984 - end of helix Processing helix chain 'V' and resid 986 through 998 removed outlier: 6.144A pdb=" N CYS V 990 " --> pdb=" O GLU V 986 " (cutoff:3.500A) Processing helix chain 'V' and resid 1001 through 1015 removed outlier: 5.189A pdb=" N GLN V1015 " --> pdb=" O MET V1011 " (cutoff:3.500A) Processing helix chain 'V' and resid 1026 through 1034 removed outlier: 6.736A pdb=" N GLN V1030 " --> pdb=" O ALA V1026 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS V1034 " --> pdb=" O GLN V1030 " (cutoff:3.500A) Processing helix chain 'V' and resid 1040 through 1055 removed outlier: 4.209A pdb=" N THR V1044 " --> pdb=" O GLY V1040 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA V1047 " --> pdb=" O LEU V1043 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR V1049 " --> pdb=" O LEU V1045 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN V1050 " --> pdb=" O LEU V1046 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP V1052 " --> pdb=" O VAL V1048 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN V1054 " --> pdb=" O ASN V1050 " (cutoff:3.500A) Processing helix chain 'V' and resid 1061 through 1066 Processing helix chain 'V' and resid 1068 through 1090 removed outlier: 3.906A pdb=" N LEU V1072 " --> pdb=" O GLN V1068 " (cutoff:3.500A) Processing helix chain 'V' and resid 1099 through 1112 removed outlier: 5.202A pdb=" N VAL V1103 " --> pdb=" O SER V1099 " (cutoff:3.500A) Processing helix chain 'V' and resid 1139 through 1145 removed outlier: 3.919A pdb=" N ASN V1143 " --> pdb=" O SER V1139 " (cutoff:3.500A) Processing helix chain 'V' and resid 1169 through 1178 Proline residue: V1178 - end of helix Processing helix chain 'V' and resid 1190 through 1197 removed outlier: 3.602A pdb=" N GLN V1195 " --> pdb=" O LYS V1191 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG V1197 " --> pdb=" O LYS V1193 " (cutoff:3.500A) Processing helix chain 'V' and resid 1212 through 1220 removed outlier: 3.649A pdb=" N ALA V1216 " --> pdb=" O ARG V1212 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG V1218 " --> pdb=" O SER V1214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG V1219 " --> pdb=" O ARG V1215 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG V1220 " --> pdb=" O ALA V1216 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 12 Processing helix chain 'W' and resid 82 through 88 removed outlier: 3.777A pdb=" N ALA W 86 " --> pdb=" O GLY W 82 " (cutoff:3.500A) Proline residue: W 88 - end of helix Processing helix chain 'W' and resid 102 through 113 removed outlier: 4.220A pdb=" N LEU W 106 " --> pdb=" O GLU W 102 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP W 107 " --> pdb=" O LEU W 103 " (cutoff:3.500A) Proline residue: W 108 - end of helix removed outlier: 4.501A pdb=" N SER W 111 " --> pdb=" O ASP W 107 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU W 112 " --> pdb=" O PRO W 108 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 102 through 113' Processing helix chain 'W' and resid 123 through 129 removed outlier: 4.037A pdb=" N ASN W 127 " --> pdb=" O ASN W 123 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS W 128 " --> pdb=" O PRO W 124 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS W 129 " --> pdb=" O VAL W 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 123 through 129' Processing helix chain 'W' and resid 130 through 140 Proline residue: W 140 - end of helix Processing helix chain 'W' and resid 151 through 163 Processing helix chain 'W' and resid 164 through 175 Processing helix chain 'W' and resid 36 through 41 Processing helix chain 'Y' and resid 19 through 33 removed outlier: 4.457A pdb=" N GLN Y 33 " --> pdb=" O ALA Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 58 through 69 removed outlier: 3.783A pdb=" N SER Y 62 " --> pdb=" O GLU Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 94 Processing helix chain 'Z' and resid 340 through 351 Processing helix chain 'Z' and resid 354 through 360 removed outlier: 3.842A pdb=" N ARG Z 358 " --> pdb=" O MET Z 354 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS Z 359 " --> pdb=" O SER Z 355 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG Z 360 " --> pdb=" O GLY Z 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 354 through 360' Processing helix chain 'Z' and resid 361 through 415 removed outlier: 3.817A pdb=" N GLN Z 372 " --> pdb=" O ARG Z 368 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS Z 412 " --> pdb=" O LYS Z 408 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP Z 413 " --> pdb=" O THR Z 409 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP Z 414 " --> pdb=" O LYS Z 410 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS Z 415 " --> pdb=" O GLY Z 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 27 removed outlier: 4.442A pdb=" N LYS a 18 " --> pdb=" O GLU a 14 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU a 21 " --> pdb=" O GLN a 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR a 26 " --> pdb=" O GLU a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 39 Processing helix chain 'a' and resid 102 through 107 removed outlier: 4.291A pdb=" N VAL a 106 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE a 107 " --> pdb=" O GLY a 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 102 through 107' Processing helix chain 'b' and resid 6 through 13 removed outlier: 4.261A pdb=" N LEU b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 78 removed outlier: 3.515A pdb=" N LEU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL b 78 " --> pdb=" O GLY b 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 73 through 78' Processing helix chain 'k' and resid 7 through 13 removed outlier: 3.988A pdb=" N ILE k 13 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 73 through 78 removed outlier: 3.725A pdb=" N LEU k 77 " --> pdb=" O ARG k 73 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL k 78 " --> pdb=" O GLY k 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 73 through 78' Processing helix chain 'c' and resid 2 through 10 removed outlier: 4.100A pdb=" N PHE c 6 " --> pdb=" O LYS c 2 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS c 9 " --> pdb=" O ARG c 5 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 66 removed outlier: 3.853A pdb=" N ILE c 65 " --> pdb=" O ARG c 61 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG c 66 " --> pdb=" O GLY c 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 61 through 66' Processing helix chain 'c' and resid 75 through 80 removed outlier: 3.627A pdb=" N LEU c 79 " --> pdb=" O PRO c 75 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 4.327A pdb=" N PHE l 6 " --> pdb=" O LYS l 2 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU l 10 " --> pdb=" O PHE l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 66 removed outlier: 3.557A pdb=" N ILE l 65 " --> pdb=" O ARG l 61 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG l 66 " --> pdb=" O GLY l 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 61 through 66' Processing helix chain 'l' and resid 75 through 80 Processing helix chain 'd' and resid 4 through 14 removed outlier: 3.715A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 69 removed outlier: 5.657A pdb=" N ARG d 69 " --> pdb=" O GLY d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 81 removed outlier: 4.585A pdb=" N LYS d 78 " --> pdb=" O PRO d 74 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN d 79 " --> pdb=" O ASP d 75 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA d 80 " --> pdb=" O MET d 76 " (cutoff:3.500A) Proline residue: d 81 - end of helix No H-bonds generated for 'chain 'd' and resid 74 through 81' Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'f' and resid 6 through 15 Processing helix chain 'q' and resid 6 through 15 Processing helix chain 'g' and resid 63 through 68 removed outlier: 3.552A pdb=" N ILE g 67 " --> pdb=" O ARG g 63 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE g 68 " --> pdb=" O GLY g 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 68' Processing helix chain 'r' and resid 63 through 68 removed outlier: 3.540A pdb=" N ILE r 67 " --> pdb=" O ARG r 63 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE r 68 " --> pdb=" O GLY r 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 63 through 68' Processing helix chain 'h' and resid 31 through 46 Processing helix chain 'h' and resid 64 through 69 Processing helix chain 'h' and resid 82 through 87 removed outlier: 3.613A pdb=" N ARG h 86 " --> pdb=" O LEU h 82 " (cutoff:3.500A) Proline residue: h 87 - end of helix No H-bonds generated for 'chain 'h' and resid 82 through 87' Processing helix chain 'h' and resid 88 through 93 removed outlier: 5.151A pdb=" N LYS h 93 " --> pdb=" O PRO h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 141 through 146 Processing helix chain 'h' and resid 162 through 168 Processing helix chain 'h' and resid 174 through 200 removed outlier: 4.326A pdb=" N HIS h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET h 179 " --> pdb=" O PRO h 175 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS h 180 " --> pdb=" O GLU h 176 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE h 181 " --> pdb=" O GLU h 177 " (cutoff:3.500A) Processing helix chain 'h' and resid 272 through 278 removed outlier: 3.503A pdb=" N ARG h 276 " --> pdb=" O ALA h 272 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN h 277 " --> pdb=" O LYS h 273 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU h 278 " --> pdb=" O TYR h 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 272 through 278' Processing helix chain 'h' and resid 311 through 317 removed outlier: 3.967A pdb=" N VAL h 315 " --> pdb=" O GLY h 311 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR h 317 " --> pdb=" O ASN h 313 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 338 removed outlier: 3.868A pdb=" N SER h 323 " --> pdb=" O GLY h 319 " (cutoff:3.500A) Processing helix chain 'h' and resid 346 through 370 Processing helix chain 'i' and resid 32 through 46 Processing helix chain 'i' and resid 119 through 124 removed outlier: 4.207A pdb=" N ASP i 123 " --> pdb=" O THR i 119 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY i 124 " --> pdb=" O GLN i 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 119 through 124' Processing helix chain 'i' and resid 135 through 145 removed outlier: 3.764A pdb=" N VAL i 145 " --> pdb=" O ARG i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 49 removed outlier: 3.540A pdb=" N LEU j 48 " --> pdb=" O GLN j 44 " (cutoff:3.500A) Proline residue: j 49 - end of helix No H-bonds generated for 'chain 'j' and resid 44 through 49' Processing helix chain 'm' and resid 13 through 27 Processing helix chain 'm' and resid 29 through 39 Processing helix chain 'm' and resid 102 through 107 removed outlier: 4.034A pdb=" N VAL m 106 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE m 107 " --> pdb=" O GLY m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 107' Processing helix chain 'n' and resid 4 through 14 removed outlier: 3.540A pdb=" N GLU n 14 " --> pdb=" O LEU n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 64 through 69 removed outlier: 3.717A pdb=" N ILE n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG n 69 " --> pdb=" O GLY n 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 64 through 69' Processing helix chain 'n' and resid 74 through 79 removed outlier: 4.466A pdb=" N LYS n 78 " --> pdb=" O PRO n 74 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN n 79 " --> pdb=" O ASP n 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 74 through 79' Processing helix chain 'o' and resid 84 through 89 removed outlier: 3.742A pdb=" N MET o 88 " --> pdb=" O THR o 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 107 Proline residue: o 107 - end of helix Processing helix chain 'o' and resid 121 through 135 Processing helix chain 'o' and resid 155 through 163 Processing helix chain 'o' and resid 209 through 228 removed outlier: 3.858A pdb=" N LYS o 228 " --> pdb=" O GLN o 224 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 28 Processing helix chain 'p' and resid 80 through 85 removed outlier: 3.932A pdb=" N ILE p 84 " --> pdb=" O LYS p 80 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR p 85 " --> pdb=" O GLY p 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 80 through 85' Processing helix chain 's' and resid 1 through 6 removed outlier: 7.055A pdb=" N GLY s 5 " --> pdb=" O MET s 1 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU s 6 " --> pdb=" O ALA s 2 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 1 through 6' Processing helix chain 's' and resid 27 through 44 Processing helix chain 's' and resid 63 through 76 removed outlier: 3.703A pdb=" N ALA s 74 " --> pdb=" O PHE s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 83 through 89 removed outlier: 4.736A pdb=" N LEU s 89 " --> pdb=" O LYS s 85 " (cutoff:3.500A) Processing helix chain 's' and resid 99 through 130 Processing helix chain 's' and resid 131 through 225 Processing helix chain 't' and resid 26 through 37 Processing helix chain 't' and resid 48 through 53 removed outlier: 5.390A pdb=" N ILE t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 138 Proline residue: t 136 - end of helix Processing helix chain 'u' and resid 26 through 37 Processing helix chain 'u' and resid 48 through 53 removed outlier: 3.633A pdb=" N LEU u 52 " --> pdb=" O SER u 48 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE u 53 " --> pdb=" O GLU u 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 48 through 53' Processing helix chain 'u' and resid 70 through 131 Processing helix chain 'v' and resid 26 through 37 Processing helix chain 'v' and resid 48 through 53 removed outlier: 5.553A pdb=" N ILE v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 65 through 70 removed outlier: 4.836A pdb=" N SER v 70 " --> pdb=" O PRO v 66 " (cutoff:3.500A) Processing helix chain 'v' and resid 71 through 138 removed outlier: 3.591A pdb=" N LYS v 135 " --> pdb=" O LEU v 131 " (cutoff:3.500A) Proline residue: v 136 - end of helix Processing helix chain 'w' and resid 26 through 37 removed outlier: 3.506A pdb=" N GLU w 31 " --> pdb=" O ARG w 27 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 53 removed outlier: 5.462A pdb=" N ILE w 53 " --> pdb=" O GLU w 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 71 removed outlier: 3.553A pdb=" N SER w 70 " --> pdb=" O PRO w 66 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE w 71 " --> pdb=" O SER w 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 66 through 71' Processing helix chain 'w' and resid 72 through 129 Processing helix chain 'y' and resid 23 through 62 removed outlier: 3.616A pdb=" N LEU y 62 " --> pdb=" O GLU y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 91 removed outlier: 4.336A pdb=" N TRP y 68 " --> pdb=" O LEU y 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 98 through 107 removed outlier: 3.500A pdb=" N GLU y 102 " --> pdb=" O VAL y 98 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE y 103 " --> pdb=" O LYS y 99 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER y 104 " --> pdb=" O LEU y 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU y 106 " --> pdb=" O GLU y 102 " (cutoff:3.500A) Processing helix chain 'y' and resid 126 through 143 removed outlier: 3.610A pdb=" N ILE y 142 " --> pdb=" O LEU y 138 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS y 143 " --> pdb=" O THR y 139 " (cutoff:3.500A) Processing helix chain 'y' and resid 145 through 157 Processing helix chain 'y' and resid 175 through 197 removed outlier: 3.993A pdb=" N LYS y 195 " --> pdb=" O GLU y 191 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR y 196 " --> pdb=" O LYS y 192 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER y 197 " --> pdb=" O ARG y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 212 through 226 Processing helix chain 'y' and resid 227 through 240 removed outlier: 5.858A pdb=" N GLU y 232 " --> pdb=" O LYS y 228 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE y 233 " --> pdb=" O TYR y 229 " (cutoff:3.500A) Processing helix chain 'y' and resid 112 through 117 removed outlier: 4.425A pdb=" N LYS y 115 " --> pdb=" O GLU y 112 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS y 116 " --> pdb=" O ARG y 113 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG y 117 " --> pdb=" O LYS y 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 112 through 117' Processing helix chain 'z' and resid 79 through 93 removed outlier: 4.143A pdb=" N SER z 83 " --> pdb=" O GLY z 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET z 84 " --> pdb=" O GLY z 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU z 85 " --> pdb=" O PHE z 81 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN z 91 " --> pdb=" O ALA z 87 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE z 92 " --> pdb=" O LEU z 88 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU z 93 " --> pdb=" O GLY z 89 " (cutoff:3.500A) Processing helix chain 'z' and resid 108 through 146 Processing helix chain 'z' and resid 154 through 180 removed outlier: 5.192A pdb=" N GLN z 158 " --> pdb=" O PRO z 154 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '7' and resid 136 through 140 removed outlier: 3.715A pdb=" N ALA 7 109 " --> pdb=" O HIS 7 158 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET 7 183 " --> pdb=" O GLN 7 108 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL 7 78 " --> pdb=" O VAL 7 214 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER 7 82 " --> pdb=" O SER 7 218 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '7' and resid 250 through 257 removed outlier: 5.504A pdb=" N SER 7 347 " --> pdb=" O LYS 7 374 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU 7 348 " --> pdb=" O GLN 7 279 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL 7 281 " --> pdb=" O LEU 7 348 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR 7 352 " --> pdb=" O PHE 7 283 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS 7 284 " --> pdb=" O SER 7 333 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '8' and resid 100 through 104 Processing sheet with id= 4, first strand: chain '9' and resid 45 through 51 removed outlier: 3.956A pdb=" N TYR 9 6 " --> pdb=" O VAL 9 91 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY 9 84 " --> pdb=" O LYS 9 103 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS 9 103 " --> pdb=" O GLY 9 84 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 9 101 " --> pdb=" O GLN 9 86 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= 6, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.387A pdb=" N GLN A 226 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG A 414 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 904 through 911 removed outlier: 4.719A pdb=" N HIS A 904 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 1086 through 1091 removed outlier: 4.180A pdb=" N ARG A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP A1093 " --> pdb=" O PHE A 981 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 6.373A pdb=" N GLY A1212 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1333 through 1338 removed outlier: 5.800A pdb=" N VAL A1333 " --> pdb=" O GLY A1356 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1552 through 1555 removed outlier: 5.462A pdb=" N ILE A1560 " --> pdb=" O LEU A1555 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1628 through 1632 removed outlier: 5.160A pdb=" N THR A1699 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY A1700 " --> pdb=" O ASN A1717 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1636 through 1640 Processing sheet with id= 14, first strand: chain 'A' and resid 1785 through 1792 removed outlier: 6.286A pdb=" N VAL A1785 " --> pdb=" O GLY A1805 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY A1805 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP A1782 " --> pdb=" O THR A1864 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1887 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1912 through 1918 Processing sheet with id= 16, first strand: chain 'A' and resid 2102 through 2106 removed outlier: 6.853A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU A2295 " --> pdb=" O ALA A2275 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2212 through 2219 Processing sheet with id= 18, first strand: chain 'A' and resid 1805 through 1812 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'A' and resid 2124 through 2129 removed outlier: 4.986A pdb=" N ILE A2124 " --> pdb=" O THR A2180 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.819A pdb=" N PHE B 435 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 446 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 449 " --> pdb=" O LEU B 685 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 685 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 686 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 826 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 785 " --> pdb=" O VAL B 810 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 498 through 503 removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 587 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 831 through 835 removed outlier: 8.534A pdb=" N THR B 831 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 840 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 1183 through 1192 removed outlier: 5.147A pdb=" N LYS B1183 " --> pdb=" O ASP B1207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B1201 " --> pdb=" O HIS B1189 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 1235 through 1243 removed outlier: 3.586A pdb=" N HIS B1235 " --> pdb=" O VAL B1225 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N SER B1217 " --> pdb=" O ALA B1243 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA B1220 " --> pdb=" O ASP B1273 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 1345 through 1350 Processing sheet with id= 26, first strand: chain 'B' and resid 1522 through 1529 Processing sheet with id= 27, first strand: chain 'B' and resid 1666 through 1671 removed outlier: 7.811A pdb=" N THR B1666 " --> pdb=" O TYR B1679 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1802 through 1805 removed outlier: 3.542A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 2017 through 2024 removed outlier: 3.952A pdb=" N GLU B2018 " --> pdb=" O GLU B2042 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL B2036 " --> pdb=" O VAL B2024 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN B2086 " --> pdb=" O ARG B2043 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 2078 through 2083 removed outlier: 6.305A pdb=" N GLY B2063 " --> pdb=" O ASP B2111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B2069 " --> pdb=" O THR B2105 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B2100 " --> pdb=" O VAL B2126 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 183 through 189 removed outlier: 5.695A pdb=" N GLY C 136 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN C 306 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 347 through 351 Processing sheet with id= 33, first strand: chain 'C' and resid 480 through 483 removed outlier: 7.958A pdb=" N LEU C 474 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 567 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 505 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP C 521 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 499 through 502 removed outlier: 6.953A pdb=" N GLY C 499 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.921A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 617 through 622 removed outlier: 4.048A pdb=" N GLU C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA C 591 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP C 652 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 662 through 666 removed outlier: 6.610A pdb=" N LYS C 872 " --> pdb=" O THR C 858 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 674 through 678 removed outlier: 3.783A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 678 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN C 683 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN C 786 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 491 through 497 removed outlier: 3.680A pdb=" N ASN C 548 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 683 through 686 Processing sheet with id= 41, first strand: chain 'C' and resid 827 through 838 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'C' and resid 859 through 863 removed outlier: 5.194A pdb=" N LEU C 868 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C3' and resid 43 through 46 removed outlier: 5.321A pdb=" N GLNC3 100 " --> pdb=" O ALAC3 90 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VALC3 86 " --> pdb=" O THRC3 104 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C3' and resid 119 through 122 removed outlier: 6.843A pdb=" N LYSC3 13 " --> pdb=" O ILEC3 122 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SERC3 2 " --> pdb=" O HISC3 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASPC3 151 " --> pdb=" O HISC3 6 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'CD' and resid 169 through 172 Processing sheet with id= 46, first strand: chain 'CE' and resid 34 through 37 removed outlier: 3.522A pdb=" N ASPCE 34 " --> pdb=" O GLUCE 53 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARGCE 6 " --> pdb=" O PHECE 54 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VALCE 7 " --> pdb=" O ALACE 82 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'CF' and resid 210 through 216 removed outlier: 3.513A pdb=" N VALCF 215 " --> pdb=" O ILECF 201 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'CN' and resid 56 through 59 Processing sheet with id= 49, first strand: chain 'CN' and resid 243 through 246 removed outlier: 4.051A pdb=" N ALACN 244 " --> pdb=" O LEUCN 239 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N CYSCN 236 " --> pdb=" O LEUCN 276 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASPCN 272 " --> pdb=" O ARGCN 240 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'CN' and resid 259 through 262 removed outlier: 6.142A pdb=" N METCN 259 " --> pdb=" O LEUCN 268 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASPCN 266 " --> pdb=" O ASPCN 261 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'F' and resid 644 through 651 removed outlier: 4.171A pdb=" N ARG F 644 " --> pdb=" O PHE F 681 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE F 646 " --> pdb=" O ASN F 679 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN F 679 " --> pdb=" O PHE F 646 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN F 674 " --> pdb=" O PHE F 751 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE F 678 " --> pdb=" O LEU F 747 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY F 743 " --> pdb=" O TYR F 682 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 692 through 699 removed outlier: 5.978A pdb=" N GLU F 693 " --> pdb=" O HIS F 711 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE F 705 " --> pdb=" O CYS F 699 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 193 through 196 removed outlier: 3.523A pdb=" N ARG J 198 " --> pdb=" O VAL J 488 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'J' and resid 208 through 212 removed outlier: 8.028A pdb=" N GLN J 217 " --> pdb=" O LEU J 233 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE J 230 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS J 237 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'J' and resid 251 through 255 removed outlier: 4.917A pdb=" N TYR J 260 " --> pdb=" O SER J 255 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS J 272 " --> pdb=" O ILE J 281 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'J' and resid 292 through 297 removed outlier: 4.943A pdb=" N VAL J 302 " --> pdb=" O HIS J 297 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR J 311 " --> pdb=" O SER J 307 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE J 314 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA J 321 " --> pdb=" O ASP J 316 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'J' and resid 334 through 339 removed outlier: 4.513A pdb=" N GLN J 344 " --> pdb=" O GLN J 339 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE J 345 " --> pdb=" O TRP J 357 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU J 356 " --> pdb=" O ARG J 365 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS J 363 " --> pdb=" O ASP J 358 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'J' and resid 377 through 381 removed outlier: 3.555A pdb=" N ALA J 377 " --> pdb=" O GLY J 390 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR J 386 " --> pdb=" O HIS J 381 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR J 385 " --> pdb=" O PHE J 400 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN J 397 " --> pdb=" O ILE J 406 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'J' and resid 418 through 421 removed outlier: 4.374A pdb=" N THR J 435 " --> pdb=" O ALA J 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN J 448 " --> pdb=" O LEU J 438 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'J' and resid 467 through 471 removed outlier: 5.434A pdb=" N ARG J 476 " --> pdb=" O ASP J 471 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 227 through 230 Processing sheet with id= 62, first strand: chain 'J' and resid 269 through 272 removed outlier: 3.538A pdb=" N ARG J 282 " --> pdb=" O CYS J 272 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 311 through 314 Processing sheet with id= 64, first strand: chain 'J' and resid 353 through 356 Processing sheet with id= 65, first strand: chain 'J' and resid 394 through 397 Processing sheet with id= 66, first strand: chain 'J' and resid 476 through 481 removed outlier: 4.179A pdb=" N THR J 485 " --> pdb=" O GLU J 481 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'K' and resid 175 through 180 removed outlier: 4.246A pdb=" N GLN K 175 " --> pdb=" O MET K 199 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'M' and resid 36 through 40 removed outlier: 5.374A pdb=" N PHE M 55 " --> pdb=" O THR M 68 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'M' and resid 261 through 265 removed outlier: 3.560A pdb=" N ALA M 270 " --> pdb=" O VAL M 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE M 274 " --> pdb=" O THR M 232 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR M 232 " --> pdb=" O PHE M 274 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'N' and resid 59 through 63 removed outlier: 4.926A pdb=" N ILE N 341 " --> pdb=" O HIS N 336 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'N' and resid 70 through 75 removed outlier: 5.640A pdb=" N THR N 80 " --> pdb=" O HIS N 75 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER N 79 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY N 85 " --> pdb=" O LEU N 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU N 89 " --> pdb=" O GLY N 85 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'N' and resid 113 through 117 removed outlier: 3.577A pdb=" N SER N 128 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR N 132 " --> pdb=" O SER N 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL N 133 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS N 145 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'N' and resid 156 through 160 removed outlier: 6.277A pdb=" N LEU N 166 " --> pdb=" O ALA N 160 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY N 174 " --> pdb=" O ASN N 192 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'N' and resid 198 through 202 removed outlier: 6.055A pdb=" N GLN N 207 " --> pdb=" O ASN N 202 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'N' and resid 240 through 244 removed outlier: 6.153A pdb=" N TYR N 249 " --> pdb=" O SER N 244 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER N 248 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS N 275 " --> pdb=" O VAL N 261 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'N' and resid 290 through 294 removed outlier: 5.433A pdb=" N ARG N 290 " --> pdb=" O GLY N 303 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA N 301 " --> pdb=" O SER N 292 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS N 299 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER N 298 " --> pdb=" O THR N 314 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE N 300 " --> pdb=" O TRP N 312 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL N 311 " --> pdb=" O LEU N 320 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG N 318 " --> pdb=" O ASP N 313 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'N' and resid 308 through 311 Processing sheet with id= 78, first strand: chain 'S' and resid 619 through 627 removed outlier: 3.552A pdb=" N GLY S 636 " --> pdb=" O VAL S 627 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'U' and resid 494 through 497 Processing sheet with id= 80, first strand: chain 'U' and resid 511 through 514 removed outlier: 5.781A pdb=" N ASN U 654 " --> pdb=" O ILE U 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP U 560 " --> pdb=" O ILE U 597 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR U 591 " --> pdb=" O THR U 566 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL U 535 " --> pdb=" O LEU U 629 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG U 536 " --> pdb=" O VAL U 520 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'U' and resid 731 through 736 removed outlier: 3.510A pdb=" N ILE U 778 " --> pdb=" O THR U 750 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'U' and resid 1033 through 1037 Processing sheet with id= 83, first strand: chain 'U' and resid 1176 through 1181 removed outlier: 3.555A pdb=" N GLN U1178 " --> pdb=" O LEU U1301 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'U' and resid 1329 through 1333 Processing sheet with id= 85, first strand: chain 'V' and resid 439 through 442 removed outlier: 5.651A pdb=" N PHE V1180 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'V' and resid 641 through 645 removed outlier: 4.755A pdb=" N GLY V 588 " --> pdb=" O SER V 717 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'V' and resid 806 through 812 Processing sheet with id= 88, first strand: chain 'V' and resid 1123 through 1127 removed outlier: 3.860A pdb=" N GLN V1131 " --> pdb=" O THR V1126 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'V' and resid 1148 through 1152 removed outlier: 4.721A pdb=" N TRP V1148 " --> pdb=" O ILE V1168 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS V1152 " --> pdb=" O GLU V1164 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU V1164 " --> pdb=" O HIS V1152 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'V' and resid 1153 through 1156 Processing sheet with id= 91, first strand: chain 'W' and resid 13 through 16 removed outlier: 4.087A pdb=" N ALA W 13 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER W 50 " --> pdb=" O LEU W 26 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR W 96 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU W 121 " --> pdb=" O LEU W 95 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Y' and resid 39 through 42 removed outlier: 3.689A pdb=" N ASP Y 39 " --> pdb=" O ILE Y 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA Y 52 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR Y 8 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE Y 72 " --> pdb=" O MET Y 79 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'a' and resid 65 through 68 Processing sheet with id= 94, first strand: chain 'a' and resid 89 through 97 removed outlier: 5.434A pdb=" N ASN a 69 " --> pdb=" O ARG a 55 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG a 55 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS a 50 " --> pdb=" O CYS a 46 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU a 43 " --> pdb=" O LEU a 110 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL a 108 " --> pdb=" O ASN a 45 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'b' and resid 40 through 43 Processing sheet with id= 96, first strand: chain 'b' and resid 65 through 68 removed outlier: 4.006A pdb=" N ARG b 65 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP b 44 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR b 30 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE b 26 " --> pdb=" O PHE b 48 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'k' and resid 40 through 43 Processing sheet with id= 98, first strand: chain 'k' and resid 45 through 49 removed outlier: 6.620A pdb=" N ARG k 16 " --> pdb=" O GLU k 83 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'c' and resid 52 through 55 removed outlier: 4.148A pdb=" N THR c 23 " --> pdb=" O LEU c 19 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR c 67 " --> pdb=" O GLU c 18 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'l' and resid 52 through 55 removed outlier: 4.031A pdb=" N THR l 23 " --> pdb=" O LEU l 19 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'd' and resid 41 through 44 Processing sheet with id=102, first strand: chain 'd' and resid 55 through 59 removed outlier: 5.598A pdb=" N ASN d 45 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS d 31 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG d 29 " --> pdb=" O THR d 47 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL d 27 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS d 16 " --> pdb=" O LEU d 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE d 70 " --> pdb=" O GLU d 21 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'e' and resid 54 through 59 removed outlier: 6.080A pdb=" N MET e 54 " --> pdb=" O GLY e 81 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY e 81 " --> pdb=" O MET e 54 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'e' and resid 71 through 75 removed outlier: 3.564A pdb=" N LYS e 72 " --> pdb=" O GLU e 63 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP e 60 " --> pdb=" O CYS e 46 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS e 46 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN e 40 " --> pdb=" O SER e 66 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'f' and resid 40 through 44 removed outlier: 7.050A pdb=" N MET f 40 " --> pdb=" O CYS f 66 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N CYS f 66 " --> pdb=" O MET f 40 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET f 42 " --> pdb=" O ILE f 64 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'f' and resid 47 through 50 removed outlier: 3.690A pdb=" N LYS f 30 " --> pdb=" O GLU f 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR f 50 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU f 28 " --> pdb=" O TYR f 50 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET f 27 " --> pdb=" O LEU f 23 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR f 71 " --> pdb=" O LYS f 22 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'q' and resid 40 through 44 removed outlier: 7.134A pdb=" N MET q 40 " --> pdb=" O CYS q 66 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS q 66 " --> pdb=" O MET q 40 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'q' and resid 47 through 50 removed outlier: 4.679A pdb=" N MET q 27 " --> pdb=" O LEU q 23 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'g' and resid 54 through 57 removed outlier: 5.857A pdb=" N CYS g 45 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS g 26 " --> pdb=" O MET g 48 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS g 16 " --> pdb=" O LEU g 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET g 69 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'r' and resid 54 through 57 removed outlier: 5.842A pdb=" N CYS r 45 " --> pdb=" O ILE r 57 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS r 26 " --> pdb=" O MET r 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG r 25 " --> pdb=" O LEU r 21 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS r 16 " --> pdb=" O LEU r 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET r 69 " --> pdb=" O LYS r 20 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'i' and resid 21 through 26 Processing sheet with id=112, first strand: chain 'i' and resid 54 through 57 removed outlier: 5.004A pdb=" N GLN i 111 " --> pdb=" O ALA i 101 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE i 97 " --> pdb=" O THR i 115 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'j' and resid 28 through 31 removed outlier: 4.158A pdb=" N VAL j 38 " --> pdb=" O CYS j 69 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'j' and resid 56 through 61 Processing sheet with id=115, first strand: chain 'j' and resid 71 through 81 removed outlier: 6.500A pdb=" N LYS j 91 " --> pdb=" O LEU j 100 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU j 98 " --> pdb=" O CYS j 93 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'j' and resid 88 through 91 Processing sheet with id=117, first strand: chain 'm' and resid 89 through 96 removed outlier: 3.684A pdb=" N VAL m 108 " --> pdb=" O ASN m 45 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'n' and resid 41 through 44 Processing sheet with id=119, first strand: chain 'n' and resid 55 through 59 removed outlier: 5.700A pdb=" N ASN n 45 " --> pdb=" O LYS n 31 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS n 31 " --> pdb=" O ASN n 45 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL n 27 " --> pdb=" O THR n 49 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS n 16 " --> pdb=" O LEU n 32 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'o' and resid 237 through 242 removed outlier: 3.521A pdb=" N HIS o 242 " --> pdb=" O LEU o 325 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU o 325 " --> pdb=" O HIS o 242 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS o 312 " --> pdb=" O SER o 308 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS o 302 " --> pdb=" O VAL o 318 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU o 303 " --> pdb=" O PHE o 297 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'o' and resid 281 through 285 removed outlier: 3.833A pdb=" N HIS o 282 " --> pdb=" O LEU o 577 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP o 284 " --> pdb=" O ILE o 575 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE o 575 " --> pdb=" O TRP o 284 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS o 565 " --> pdb=" O HIS o 559 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'o' and resid 336 through 341 removed outlier: 6.216A pdb=" N GLN o 346 " --> pdb=" O ASN o 341 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR o 345 " --> pdb=" O THR o 361 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU o 358 " --> pdb=" O ILE o 367 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN o 365 " --> pdb=" O ASP o 360 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'o' and resid 378 through 381 removed outlier: 3.665A pdb=" N CYS o 378 " --> pdb=" O GLY o 394 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN o 389 " --> pdb=" O ILE o 405 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS o 399 " --> pdb=" O MET o 395 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN o 402 " --> pdb=" O VAL o 411 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU o 409 " --> pdb=" O ASP o 404 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'o' and resid 423 through 427 removed outlier: 3.595A pdb=" N THR o 423 " --> pdb=" O THR o 436 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS o 454 " --> pdb=" O VAL o 444 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'o' and resid 466 through 470 removed outlier: 4.731A pdb=" N ALA o 466 " --> pdb=" O GLN o 479 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP o 475 " --> pdb=" O SER o 470 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS o 474 " --> pdb=" O ALA o 490 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN o 484 " --> pdb=" O SER o 480 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'o' and resid 514 through 517 removed outlier: 4.975A pdb=" N TYR o 522 " --> pdb=" O SER o 517 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER o 521 " --> pdb=" O TRP o 537 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE o 534 " --> pdb=" O TYR o 543 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS o 541 " --> pdb=" O ASP o 536 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'o' and resid 355 through 358 removed outlier: 3.672A pdb=" N SER o 368 " --> pdb=" O LEU o 358 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'o' and resid 399 through 402 Processing sheet with id=129, first strand: chain 'o' and resid 530 through 534 removed outlier: 4.800A pdb=" N GLY o 530 " --> pdb=" O ALA o 548 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'p' and resid 56 through 59 Processing sheet with id=131, first strand: chain 'p' and resid 69 through 75 removed outlier: 3.763A pdb=" N SER p 70 " --> pdb=" O HIS p 65 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA p 61 " --> pdb=" O LEU p 74 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP p 60 " --> pdb=" O CYS p 46 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS p 46 " --> pdb=" O ASP p 60 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN p 40 " --> pdb=" O SER p 66 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG p 30 " --> pdb=" O VAL p 90 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU p 86 " --> pdb=" O TRP p 34 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 't' and resid 38 through 41 removed outlier: 4.957A pdb=" N GLY t 38 " --> pdb=" O LEU t 47 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN t 45 " --> pdb=" O ASP t 40 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'w' and resid 16 through 19 removed outlier: 3.729A pdb=" N HIS w 23 " --> pdb=" O SER w 18 " (cutoff:3.500A) 6787 hydrogen bonds defined for protein. 20133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 263 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 198 stacking parallelities Total time for adding SS restraints: 80.21 Time building geometry restraints manager: 39.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 20194 1.32 - 1.44: 31846 1.44 - 1.57: 60718 1.57 - 1.69: 928 1.69 - 1.82: 494 Bond restraints: 114180 Sorted by residual: bond pdb=" O2P SEP K 224 " pdb=" P SEP K 224 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3P SEP K 232 " pdb=" P SEP K 232 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O2P SEP K 232 " pdb=" P SEP K 232 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O1P SEP K 232 " pdb=" P SEP K 232 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O1P SEP K 224 " pdb=" P SEP K 224 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 114175 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.66: 4129 104.66 - 112.17: 48424 112.17 - 119.67: 39311 119.67 - 127.18: 60130 127.18 - 134.69: 2026 Bond angle restraints: 154020 Sorted by residual: angle pdb=" PB ATP 7 502 " pdb=" O3B ATP 7 502 " pdb=" PG ATP 7 502 " ideal model delta sigma weight residual 139.87 128.67 11.20 1.00e+00 1.00e+00 1.26e+02 angle pdb=" PA ATP 7 502 " pdb=" O3A ATP 7 502 " pdb=" PB ATP 7 502 " ideal model delta sigma weight residual 136.83 128.97 7.86 1.00e+00 1.00e+00 6.19e+01 angle pdb=" C CYS M 24 " pdb=" CA CYS M 24 " pdb=" CB CYS M 24 " ideal model delta sigma weight residual 113.33 100.66 12.67 2.26e+00 1.96e-01 3.14e+01 angle pdb=" N GLN M 25 " pdb=" CA GLN M 25 " pdb=" C GLN M 25 " ideal model delta sigma weight residual 112.92 106.61 6.31 1.23e+00 6.61e-01 2.63e+01 angle pdb=" N CYS M 27 " pdb=" CA CYS M 27 " pdb=" C CYS M 27 " ideal model delta sigma weight residual 113.28 107.78 5.50 1.22e+00 6.72e-01 2.03e+01 ... (remaining 154015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 57065 35.79 - 71.59: 1369 71.59 - 107.38: 193 107.38 - 143.17: 12 143.17 - 178.97: 25 Dihedral angle restraints: 58664 sinusoidal: 24328 harmonic: 34336 Sorted by residual: dihedral pdb=" O4' U I 162 " pdb=" C1' U I 162 " pdb=" N1 U I 162 " pdb=" C2 U I 162 " ideal model delta sinusoidal sigma weight residual 200.00 26.84 173.16 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U I 176 " pdb=" C1' U I 176 " pdb=" N1 U I 176 " pdb=" C2 U I 176 " ideal model delta sinusoidal sigma weight residual 200.00 40.33 159.67 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' U I 174 " pdb=" C1' U I 174 " pdb=" N1 U I 174 " pdb=" C2 U I 174 " ideal model delta sinusoidal sigma weight residual 200.00 48.74 151.26 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 58661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 11326 0.060 - 0.121: 1526 0.121 - 0.181: 98 0.181 - 0.242: 4 0.242 - 0.302: 6 Chirality restraints: 12960 Sorted by residual: chirality pdb=" CB ILE C 949 " pdb=" CA ILE C 949 " pdb=" CG1 ILE C 949 " pdb=" CG2 ILE C 949 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" P G 5 95 " pdb=" OP1 G 5 95 " pdb=" OP2 G 5 95 " pdb=" O5' G 5 95 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 -2.62 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 12957 not shown) Planarity restraints: 21144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS u 64 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.41e+01 pdb=" N PRO u 65 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO u 65 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO u 65 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR h 163 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR h 163 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR h 163 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP h 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 7 337 " -0.011 2.00e-02 2.50e+03 1.96e-02 9.58e+00 pdb=" CG TRP 7 337 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP 7 337 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP 7 337 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 7 337 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP 7 337 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 7 337 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 7 337 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP 7 337 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP 7 337 " 0.009 2.00e-02 2.50e+03 ... (remaining 21141 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 111 2.30 - 3.01: 62491 3.01 - 3.72: 199207 3.72 - 4.43: 302788 4.43 - 5.14: 460966 Nonbonded interactions: 1025563 Sorted by model distance: nonbonded pdb=" P G I 1 " pdb=" O2' A I 152 " model vdw 1.589 3.400 nonbonded pdb="MG MG C1501 " pdb=" O2B GTP C1502 " model vdw 1.931 2.170 nonbonded pdb="MG MG C1501 " pdb=" O2G GTP C1502 " model vdw 1.937 2.170 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C1501 " model vdw 1.963 2.170 nonbonded pdb=" OP1 A 6 53 " pdb="MG MG 6 207 " model vdw 1.966 2.170 ... (remaining 1025558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 13 or (resid 14 through 27 and (name N or name CA or name \ C or name O )) or resid 28 or (resid 29 through 77 and (name N or name CA or nam \ e C or name O )) or resid 78 or (resid 87 through 88 and (name N or name CA or n \ ame C or name O )) or resid 89 or (resid 90 through 112 and (name N or name CA o \ r name C or name O )) or resid 113 or (resid 114 through 115 and (name N or name \ CA or name C or name O )))) selection = chain 'm' } ncs_group { reference = (chain 'b' and ((resid 6 through 52 and (name N or name CA or name C or name O ) \ ) or resid 53 or (resid 54 through 84 and (name N or name CA or name C or name O \ )) or resid 85 through 87)) selection = chain 'k' } ncs_group { reference = (chain 'c' and ((resid 1 through 51 and (name N or name CA or name C or name O ) \ ) or resid 52 or (resid 53 through 70 and (name N or name CA or name C or name O \ )) or resid 71 or (resid 72 through 74 and (name N or name CA or name C or name \ O )) or resid 75 or (resid 76 through 80 and (name N or name CA or name C or na \ me O )))) selection = chain 'l' } ncs_group { reference = (chain 'd' and ((resid 2 through 5 and (name N or name CA or name C or name O )) \ or resid 6 or (resid 7 through 73 and (name N or name CA or name C or name O )) \ or resid 74 or (resid 75 through 80 and (name N or name CA or name C or name O \ )) or resid 81 or (resid 82 through 84 and (name N or name CA or name C or name \ O )))) selection = chain 'n' } ncs_group { reference = (chain 'e' and ((resid 13 through 16 and (name N or name CA or name C or name O \ )) or resid 17 or (resid 18 through 91 and (name N or name CA or name C or name \ O )))) selection = (chain 'p' and resid 13 through 91) } ncs_group { reference = (chain 'f' and (resid 4 or (resid 5 through 6 and (name N or name CA or name C o \ r name O )) or resid 7 or (resid 8 and (name N or name CA or name C or name O )) \ or resid 9 or (resid 10 through 17 and (name N or name CA or name C or name O ) \ ) or resid 18 or (resid 19 through 75 and (name N or name CA or name C or name O \ )))) selection = chain 'q' } ncs_group { reference = (chain 'g' and ((resid 4 through 5 and (name N or name CA or name C or name O )) \ or resid 6 through 7 or (resid 8 through 35 and (name N or name CA or name C or \ name O )) or resid 36 or (resid 37 through 75 and (name N or name CA or name C \ or name O )) or (resid 76 and (name N or name CA or name C or name O or name OXT \ )))) selection = chain 'r' } ncs_group { reference = (chain 't' and resid 2 through 131) selection = chain 'u' selection = (chain 'v' and resid 2 through 131) selection = (chain 'w' and resid 2 through 131) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.370 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: 40.080 Check model and map are aligned: 1.200 Set scattering table: 0.760 Process input model: 375.130 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.620 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 442.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.003 0.101 114180 Z= 0.183 Angle : 0.524 12.674 154020 Z= 0.293 Chirality : 0.041 0.302 12960 Planarity : 0.004 0.094 21144 Dihedral : 14.885 178.965 41358 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.74 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.31 (0.07), residues: 16632 helix: 1.98 (0.06), residues: 7294 sheet: 0.45 (0.12), residues: 2167 loop : -0.09 (0.07), residues: 7171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 7 337 HIS 0.007 0.001 HIS A1966 PHE 0.026 0.001 PHE V1217 TYR 0.018 0.001 TYR S 155 ARG 0.008 0.000 ARG 4 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 588 time to evaluate : 9.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 592 average time/residue: 1.3230 time to fit residues: 1199.4839 Evaluate side-chains 532 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 530 time to evaluate : 9.243 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 12.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1434 optimal weight: 50.0000 chunk 1287 optimal weight: 50.0000 chunk 714 optimal weight: 7.9990 chunk 439 optimal weight: 0.9980 chunk 868 optimal weight: 4.9990 chunk 687 optimal weight: 50.0000 chunk 1331 optimal weight: 8.9990 chunk 515 optimal weight: 3.9990 chunk 809 optimal weight: 3.9990 chunk 991 optimal weight: 1.9990 chunk 1542 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A1018 ASN C 87 GLN D 110 GLN F 711 HIS H 240 ASN ** H 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 451 HIS ** M 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN S 265 GLN ** i 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 212 ASN y 215 ASN z 114 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 114180 Z= 0.272 Angle : 0.525 10.089 154020 Z= 0.273 Chirality : 0.043 0.331 12960 Planarity : 0.004 0.086 21144 Dihedral : 14.298 178.073 24175 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 0.55 % Allowed : 4.41 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.48 (0.07), residues: 16632 helix: 2.19 (0.06), residues: 7483 sheet: 0.35 (0.11), residues: 2142 loop : -0.08 (0.08), residues: 7007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 315 HIS 0.010 0.001 HIS F 711 PHE 0.018 0.002 PHE A1099 TYR 0.022 0.001 TYR J 385 ARG 0.006 0.000 ARG z 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 538 time to evaluate : 9.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 558 average time/residue: 1.3382 time to fit residues: 1156.9603 Evaluate side-chains 542 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 526 time to evaluate : 9.224 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.1564 time to fit residues: 21.6012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 857 optimal weight: 3.9990 chunk 478 optimal weight: 10.0000 chunk 1284 optimal weight: 4.9990 chunk 1050 optimal weight: 50.0000 chunk 425 optimal weight: 10.0000 chunk 1545 optimal weight: 8.9990 chunk 1669 optimal weight: 20.0000 chunk 1376 optimal weight: 7.9990 chunk 1532 optimal weight: 8.9990 chunk 526 optimal weight: 3.9990 chunk 1239 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A1124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS F 711 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 532 GLN J 370 ASN J 451 HIS L 116 ASN ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN ** i 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 82 ASN o 472 ASN z 114 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 114180 Z= 0.572 Angle : 0.643 13.945 154020 Z= 0.331 Chirality : 0.051 0.336 12960 Planarity : 0.005 0.109 21144 Dihedral : 14.364 179.918 24175 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 0.97 % Allowed : 7.36 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.13 % 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: 1.30 (0.07), residues: 16632 helix: 2.10 (0.06), residues: 7503 sheet: -0.01 (0.11), residues: 2153 loop : -0.17 (0.08), residues: 6976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP h 170 HIS 0.011 0.002 HIS A1966 PHE 0.046 0.003 PHE M 103 TYR 0.030 0.002 TYR A 614 ARG 0.010 0.001 ARG y 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 527 time to evaluate : 9.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 36 residues processed: 576 average time/residue: 1.3124 time to fit residues: 1183.6272 Evaluate side-chains 553 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 517 time to evaluate : 9.257 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 1.1555 time to fit residues: 25.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1527 optimal weight: 2.9990 chunk 1162 optimal weight: 4.9990 chunk 802 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 737 optimal weight: 7.9990 chunk 1037 optimal weight: 50.0000 chunk 1551 optimal weight: 3.9990 chunk 1642 optimal weight: 50.0000 chunk 810 optimal weight: 0.9990 chunk 1470 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 52 GLN ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A 97 HIS A 361 HIS A1857 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN N 101 ASN ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN ** i 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 114180 Z= 0.249 Angle : 0.509 10.861 154020 Z= 0.260 Chirality : 0.042 0.256 12960 Planarity : 0.004 0.075 21144 Dihedral : 14.270 178.022 24175 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 1.31 % Allowed : 8.19 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.13 % 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: 1.55 (0.07), residues: 16632 helix: 2.38 (0.06), residues: 7515 sheet: 0.09 (0.11), residues: 2140 loop : -0.12 (0.08), residues: 6977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 315 HIS 0.005 0.001 HIS C 928 PHE 0.018 0.002 PHE H 587 TYR 0.026 0.001 TYR D 95 ARG 0.007 0.000 ARG A1523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 528 time to evaluate : 9.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 46 residues processed: 604 average time/residue: 1.3172 time to fit residues: 1232.1687 Evaluate side-chains 560 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 514 time to evaluate : 9.227 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 43 residues processed: 3 average time/residue: 0.8679 time to fit residues: 16.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1367 optimal weight: 4.9990 chunk 932 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 1222 optimal weight: 30.0000 chunk 677 optimal weight: 2.9990 chunk 1401 optimal weight: 50.0000 chunk 1135 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 838 optimal weight: 0.9980 chunk 1474 optimal weight: 0.2980 chunk 414 optimal weight: 0.0870 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 363 HIS ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A 97 HIS F 711 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN H 532 GLN ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN z 114 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 114180 Z= 0.196 Angle : 0.483 10.996 154020 Z= 0.244 Chirality : 0.041 0.232 12960 Planarity : 0.004 0.073 21144 Dihedral : 14.163 177.838 24175 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.37 % Allowed : 9.19 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.75 (0.07), residues: 16632 helix: 2.59 (0.06), residues: 7546 sheet: 0.12 (0.11), residues: 2221 loop : -0.06 (0.08), residues: 6865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 315 HIS 0.011 0.001 HIS F 711 PHE 0.023 0.001 PHE V1217 TYR 0.018 0.001 TYR o 81 ARG 0.011 0.000 ARG 4 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 530 time to evaluate : 9.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 53 residues processed: 611 average time/residue: 1.3160 time to fit residues: 1271.2602 Evaluate side-chains 570 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 517 time to evaluate : 9.259 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 47 residues processed: 6 average time/residue: 1.1309 time to fit residues: 23.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 552 optimal weight: 0.3980 chunk 1478 optimal weight: 0.9980 chunk 324 optimal weight: 40.0000 chunk 964 optimal weight: 40.0000 chunk 405 optimal weight: 0.0980 chunk 1643 optimal weight: 0.2980 chunk 1364 optimal weight: 20.0000 chunk 761 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 543 optimal weight: 5.9990 chunk 862 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 363 HIS ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A 97 HIS A 659 GLN C 642 HIS D 91 GLN F 711 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 GLN T 628 GLN V 409 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 114180 Z= 0.131 Angle : 0.462 12.458 154020 Z= 0.232 Chirality : 0.040 0.215 12960 Planarity : 0.003 0.070 21144 Dihedral : 14.073 179.401 24175 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 9.59 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.95 (0.07), residues: 16632 helix: 2.79 (0.06), residues: 7540 sheet: 0.22 (0.11), residues: 2217 loop : -0.01 (0.08), residues: 6875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 398 HIS 0.010 0.001 HIS F 711 PHE 0.016 0.001 PHE 4 56 TYR 0.033 0.001 TYR S 205 ARG 0.005 0.000 ARG h 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 540 time to evaluate : 9.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 53 residues processed: 627 average time/residue: 1.2945 time to fit residues: 1280.7031 Evaluate side-chains 578 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 525 time to evaluate : 9.230 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 50 residues processed: 3 average time/residue: 0.8373 time to fit residues: 16.9532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1584 optimal weight: 50.0000 chunk 185 optimal weight: 1.9990 chunk 936 optimal weight: 1.9990 chunk 1200 optimal weight: 50.0000 chunk 930 optimal weight: 2.9990 chunk 1383 optimal weight: 40.0000 chunk 917 optimal weight: 6.9990 chunk 1637 optimal weight: 6.9990 chunk 1024 optimal weight: 7.9990 chunk 998 optimal weight: 3.9990 chunk 756 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 363 HIS ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A 659 GLN A 757 ASN F 711 HIS K 104 GLN T 628 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 114180 Z= 0.262 Angle : 0.497 12.924 154020 Z= 0.250 Chirality : 0.042 0.234 12960 Planarity : 0.004 0.068 21144 Dihedral : 14.039 179.005 24175 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 10.29 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.95 (0.07), residues: 16632 helix: 2.79 (0.06), residues: 7552 sheet: 0.18 (0.11), residues: 2242 loop : 0.00 (0.08), residues: 6838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 7 337 HIS 0.011 0.001 HIS F 711 PHE 0.025 0.002 PHE 7 232 TYR 0.029 0.001 TYR D 95 ARG 0.008 0.000 ARG h 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 531 time to evaluate : 9.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 54 residues processed: 603 average time/residue: 1.3063 time to fit residues: 1239.0624 Evaluate side-chains 578 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 524 time to evaluate : 9.214 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 52 residues processed: 2 average time/residue: 1.2871 time to fit residues: 16.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1013 optimal weight: 7.9990 chunk 653 optimal weight: 40.0000 chunk 978 optimal weight: 0.9990 chunk 493 optimal weight: 0.3980 chunk 321 optimal weight: 50.0000 chunk 317 optimal weight: 40.0000 chunk 1041 optimal weight: 10.0000 chunk 1115 optimal weight: 5.9990 chunk 809 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 1287 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS C 248 GLN N 116 HIS ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN ** i 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 114180 Z= 0.271 Angle : 0.508 13.329 154020 Z= 0.256 Chirality : 0.043 0.253 12960 Planarity : 0.004 0.067 21144 Dihedral : 14.043 179.171 24175 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.29 % Allowed : 10.51 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.95 (0.07), residues: 16632 helix: 2.79 (0.06), residues: 7553 sheet: 0.18 (0.11), residues: 2234 loop : -0.01 (0.08), residues: 6845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 7 337 HIS 0.006 0.001 HIS 8 103 PHE 0.021 0.001 PHE A 616 TYR 0.028 0.001 TYR D 95 ARG 0.007 0.000 ARG h 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 527 time to evaluate : 9.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 59 residues processed: 604 average time/residue: 1.3266 time to fit residues: 1264.6451 Evaluate side-chains 586 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 527 time to evaluate : 8.334 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 57 residues processed: 2 average time/residue: 0.7927 time to fit residues: 14.0376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1489 optimal weight: 40.0000 chunk 1568 optimal weight: 0.7980 chunk 1431 optimal weight: 20.0000 chunk 1525 optimal weight: 6.9990 chunk 918 optimal weight: 9.9990 chunk 664 optimal weight: 0.6980 chunk 1198 optimal weight: 0.9990 chunk 468 optimal weight: 30.0000 chunk 1378 optimal weight: 7.9990 chunk 1443 optimal weight: 1.9990 chunk 1520 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS F 711 HIS ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN V1195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 114180 Z= 0.258 Angle : 0.507 13.737 154020 Z= 0.254 Chirality : 0.042 0.247 12960 Planarity : 0.004 0.066 21144 Dihedral : 14.027 179.130 24175 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.18 % Allowed : 10.61 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 1.97 (0.07), residues: 16632 helix: 2.82 (0.06), residues: 7553 sheet: 0.18 (0.11), residues: 2227 loop : 0.00 (0.08), residues: 6852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 7 337 HIS 0.010 0.001 HIS F 711 PHE 0.023 0.001 PHE 4 56 TYR 0.030 0.001 TYR D 95 ARG 0.005 0.000 ARG h 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 530 time to evaluate : 9.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 66 residues processed: 603 average time/residue: 1.3753 time to fit residues: 1315.6567 Evaluate side-chains 590 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 524 time to evaluate : 9.309 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 62 residues processed: 5 average time/residue: 1.3970 time to fit residues: 23.2434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1002 optimal weight: 0.6980 chunk 1613 optimal weight: 50.0000 chunk 984 optimal weight: 2.9990 chunk 765 optimal weight: 1.9990 chunk 1121 optimal weight: 40.0000 chunk 1692 optimal weight: 10.0000 chunk 1557 optimal weight: 1.9990 chunk 1347 optimal weight: 40.0000 chunk 139 optimal weight: 0.9990 chunk 1041 optimal weight: 7.9990 chunk 826 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS A1121 ASN CN 277 GLN K 104 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 114180 Z= 0.182 Angle : 0.485 13.400 154020 Z= 0.241 Chirality : 0.041 0.223 12960 Planarity : 0.003 0.066 21144 Dihedral : 13.988 179.033 24175 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 1.04 % Allowed : 10.86 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 2.06 (0.07), residues: 16632 helix: 2.91 (0.06), residues: 7556 sheet: 0.25 (0.11), residues: 2229 loop : 0.02 (0.08), residues: 6847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 7 337 HIS 0.006 0.001 HIS 8 103 PHE 0.016 0.001 PHE H 587 TYR 0.029 0.001 TYR D 95 ARG 0.005 0.000 ARG h 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33264 Ramachandran restraints generated. 16632 Oldfield, 0 Emsley, 16632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 533 time to evaluate : 9.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 61 residues processed: 600 average time/residue: 1.3753 time to fit residues: 1311.8648 Evaluate side-chains 588 residues out of total 14953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 527 time to evaluate : 9.259 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 61 residues processed: 1 average time/residue: 1.7616 time to fit residues: 14.9228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1699 random chunks: chunk 1070 optimal weight: 50.0000 chunk 1435 optimal weight: 50.0000 chunk 412 optimal weight: 20.0000 chunk 1242 optimal weight: 30.0000 chunk 199 optimal weight: 3.9990 chunk 374 optimal weight: 0.0370 chunk 1349 optimal weight: 40.0000 chunk 564 optimal weight: 0.9990 chunk 1386 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 103 HIS K 104 GLN N 56 GLN ** N 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 GLN ** S 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.112182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.083821 restraints weight = 440579.279| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.46 r_work: 0.3318 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 62 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 62 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 114180 Z= 0.215 Angle : 0.493 16.809 154020 Z= 0.246 Chirality : 0.041 0.228 12960 Planarity : 0.003 0.066 21144 Dihedral : 13.964 179.393 24175 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 1.04 % Allowed : 10.81 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: 2.06 (0.07), residues: 16632 helix: 2.91 (0.06), residues: 7562 sheet: 0.22 (0.11), residues: 2245 loop : 0.02 (0.08), residues: 6825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 7 337 HIS 0.006 0.001 HIS 8 103 PHE 0.021 0.001 PHE 4 56 TYR 0.029 0.001 TYR D 95 ARG 0.005 0.000 ARG h 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28625.17 seconds wall clock time: 497 minutes 36.73 seconds (29856.73 seconds total)