Starting phenix.real_space_refine on Sun Mar 17 01:31:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ylz_6839/03_2024/5ylz_6839_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 382 5.49 5 Mg 6 5.21 5 S 251 5.16 5 C 46951 2.51 5 N 13254 2.21 5 O 15397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A PHE 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1490": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A GLU 1582": "OE1" <-> "OE2" Residue "A PHE 1606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "H GLU 609": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "L ARG 151": "NH1" <-> "NH2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T GLU 236": "OE1" <-> "OE2" Residue "T GLU 321": "OE1" <-> "OE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "M ARG 261": "NH1" <-> "NH2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "P ARG 135": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q ARG 125": "NH1" <-> "NH2" Residue "Q ARG 185": "NH1" <-> "NH2" Residue "S ARG 382": "NH1" <-> "NH2" Residue "S ARG 439": "NH1" <-> "NH2" Residue "U GLU 83": "OE1" <-> "OE2" Residue "U GLU 104": "OE1" <-> "OE2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 175": "OE1" <-> "OE2" Residue "W GLU 295": "OE1" <-> "OE2" Residue "W ARG 442": "NH1" <-> "NH2" Residue "W GLU 444": "OE1" <-> "OE2" Residue "W GLU 456": "OE1" <-> "OE2" Residue "W GLU 458": "OE1" <-> "OE2" Residue "W ARG 461": "NH1" <-> "NH2" Residue "W ARG 471": "NH1" <-> "NH2" Residue "W ARG 480": "NH1" <-> "NH2" Residue "W ARG 489": "NH1" <-> "NH2" Residue "W ARG 497": "NH1" <-> "NH2" Residue "W ARG 537": "NH1" <-> "NH2" Residue "W ARG 538": "NH1" <-> "NH2" Residue "W ARG 547": "NH1" <-> "NH2" Residue "W ARG 565": "NH1" <-> "NH2" Residue "W ARG 575": "NH1" <-> "NH2" Residue "W ARG 586": "NH1" <-> "NH2" Residue "W GLU 587": "OE1" <-> "OE2" Residue "W GLU 604": "OE1" <-> "OE2" Residue "W ARG 608": "NH1" <-> "NH2" Residue "W ARG 626": "NH1" <-> "NH2" Residue "W GLU 663": "OE1" <-> "OE2" Residue "W GLU 709": "OE1" <-> "OE2" Residue "W ARG 714": "NH1" <-> "NH2" Residue "W GLU 744": "OE1" <-> "OE2" Residue "W ARG 751": "NH1" <-> "NH2" Residue "W GLU 761": "OE1" <-> "OE2" Residue "W ARG 786": "NH1" <-> "NH2" Residue "W GLU 790": "OE1" <-> "OE2" Residue "W ARG 805": "NH1" <-> "NH2" Residue "W ARG 808": "NH1" <-> "NH2" Residue "W ARG 811": "NH1" <-> "NH2" Residue "W ARG 819": "NH1" <-> "NH2" Residue "W ARG 840": "NH1" <-> "NH2" Residue "W GLU 878": "OE1" <-> "OE2" Residue "W ARG 909": "NH1" <-> "NH2" Residue "W ARG 938": "NH1" <-> "NH2" Residue "W ARG 942": "NH1" <-> "NH2" Residue "W ARG 969": "NH1" <-> "NH2" Residue "W ARG 988": "NH1" <-> "NH2" Residue "W ARG 992": "NH1" <-> "NH2" Residue "W ARG 994": "NH1" <-> "NH2" Residue "W ARG 1022": "NH1" <-> "NH2" Residue "W ARG 1036": "NH1" <-> "NH2" Residue "W GLU 1050": "OE1" <-> "OE2" Residue "W GLU 1065": "OE1" <-> "OE2" Residue "W ARG 1077": "NH1" <-> "NH2" Residue "W GLU 1087": "OE1" <-> "OE2" Residue "W GLU 1105": "OE1" <-> "OE2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a GLU 90": "OE1" <-> "OE2" Residue "c ARG 82": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ARG 97": "NH1" <-> "NH2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "j ARG 82": "NH1" <-> "NH2" Residue "k ARG 30": "NH1" <-> "NH2" Residue "m ARG 88": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n GLU 70": "OE1" <-> "OE2" Residue "n ARG 97": "NH1" <-> "NH2" Residue "q GLU 24": "OE1" <-> "OE2" Residue "q GLU 29": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "r GLU 24": "OE1" <-> "OE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r GLU 48": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 129": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 29": "OE1" <-> "OE2" Residue "s GLU 48": "OE1" <-> "OE2" Residue "s GLU 129": "OE1" <-> "OE2" Residue "s GLU 132": "OE1" <-> "OE2" Residue "t GLU 24": "OE1" <-> "OE2" Residue "t GLU 29": "OE1" <-> "OE2" Residue "t GLU 48": "OE1" <-> "OE2" Residue "t GLU 94": "OE1" <-> "OE2" Residue "t GLU 129": "OE1" <-> "OE2" Residue "t GLU 132": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76247 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 15931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1931, 15931 Classifications: {'peptide': 1931} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 100, 'TRANS': 1830} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2465 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 39, 'rna3p_pyr': 56} Link IDs: {'rna2p': 22, 'rna3p': 94} Chain breaks: 2 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7019 Classifications: {'peptide': 878} Link IDs: {'PTRANS': 49, 'TRANS': 828} Chain breaks: 2 Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 21, 'rna3p': 81} Chain: "E" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1310 Classifications: {'RNA': 62} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 11, 'rna3p_pur': 26, 'rna3p_pyr': 19} Link IDs: {'rna2p': 16, 'rna3p': 45} Chain breaks: 4 Chain: "F" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1909 Classifications: {'RNA': 91} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 16, 'rna3p_pur': 29, 'rna3p_pyr': 40} Link IDs: {'rna2p': 22, 'rna3p': 68} Chain breaks: 2 Chain: "G" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 258 Chain: "H" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 3012 Classifications: {'peptide': 562} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 392} Link IDs: {'PTRANS': 22, 'TRANS': 539} Chain breaks: 32 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1720 Unresolved non-hydrogen angles: 2228 Unresolved non-hydrogen dihedrals: 1449 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 26, 'ASN:plan1': 22, 'TRP:plan': 11, 'ASP:plan': 28, 'PHE:plan': 21, 'GLU:plan': 53, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 965 Chain: "I" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3424 Classifications: {'peptide': 517} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 249} Link IDs: {'PTRANS': 11, 'TRANS': 505} Chain breaks: 17 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1062 Unresolved non-hydrogen angles: 1365 Unresolved non-hydrogen dihedrals: 913 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 3, 'TYR:plan': 18, 'ASN:plan1': 8, 'TRP:plan': 8, 'ASP:plan': 19, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 638 Chain: "J" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 2949 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 8 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 802 Unresolved non-hydrogen dihedrals: 503 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 13, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 372 Chain: "K" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 777 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain breaks: 1 Chain: "L" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "T" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2357 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 325} Chain breaks: 8 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 10, 'TYR:plan': 10, 'ASN:plan1': 13, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 297 Chain: "M" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1472 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 3 Chain: "N" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2089 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "O" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2646 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "P" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1583 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "S" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1701 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain: "U" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1202 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain breaks: 1 Chain: "V" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 554 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "W" Number of atoms: 5553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5553 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 670} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "a" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "b" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "c" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "g" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "h" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "i" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "j" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 616 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "m" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "n" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 528 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "o" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 841 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 167 Chain: "p" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 513 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 850 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "s" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "t" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 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: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 42802 SG CYS L 104 53.114 180.900 118.355 1.00 76.55 S ATOM 42808 SG CYS L 105 56.110 183.192 119.582 1.00 86.15 S ATOM 42833 SG CYS L 108 56.687 179.586 117.986 1.00 79.61 S ATOM 43147 SG CYS L 148 56.172 180.359 121.050 1.00 72.13 S ATOM 42802 SG CYS L 104 53.114 180.900 118.355 1.00 76.55 S ATOM 42936 SG CYS L 122 53.674 177.873 116.844 1.00 75.28 S ATOM 43157 SG CYS L 150 50.455 178.385 117.839 1.00150.24 S ATOM 43178 SG CYS L 153 51.488 180.965 115.224 1.00 83.55 S ATOM 42833 SG CYS L 108 56.687 179.586 117.986 1.00 79.61 S ATOM 42922 SG CYS L 120 57.366 176.154 117.093 1.00 91.66 S ATOM 42936 SG CYS L 122 53.674 177.873 116.844 1.00 75.28 S ATOM 43124 SG CYS L 145 55.690 176.547 119.994 1.00 49.41 S ATOM 45647 SG CYS M 13 63.644 145.882 118.399 1.00181.55 S ATOM 46105 SG CYS M 71 66.837 145.104 120.019 1.00168.29 S ATOM 46120 SG CYS M 73 64.702 147.448 121.468 1.00127.23 S ATOM 46126 SG CYS M 74 63.499 144.321 121.554 1.00138.45 S ATOM 45805 SG CYS M 34 77.546 147.850 127.622 1.00119.02 S ATOM 45828 SG CYS M 37 81.002 147.654 128.710 1.00148.17 S ATOM 46027 SG CYS M 61 80.298 148.053 125.340 1.00112.99 S ATOM 46051 SG CYS M 64 79.583 144.541 127.289 1.00134.20 S ATOM 47616 SG CYS N 73 52.485 161.171 138.342 1.00170.13 S ATOM 47678 SG CYS N 81 51.212 164.553 138.989 1.00164.99 S ATOM 47718 SG CYS N 87 51.665 163.075 135.278 1.00120.64 S Time building chain proxies: 29.75, per 1000 atoms: 0.39 Number of scatterers: 76247 At special positions: 0 Unit cell: (222.6, 269.24, 277.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 251 16.00 P 382 15.00 Mg 6 11.99 O 15397 8.00 N 13254 7.00 C 46951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.94 Conformation dependent library (CDL) restraints added in 9.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb=" ZN M 400 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 74 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 13 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 73 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 71 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 64 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 61 " pdb=" ZN N 400 " pdb="ZN ZN N 400 " - pdb=" SG CYS N 73 " pdb="ZN ZN N 400 " - pdb=" SG CYS N 81 " pdb="ZN ZN N 400 " - pdb=" NE2 HIS N 91 " pdb="ZN ZN N 400 " - pdb=" SG CYS N 87 " Number of angles added : 33 17606 Ramachandran restraints generated. 8803 Oldfield, 0 Emsley, 8803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 79 sheets defined 43.2% alpha, 10.2% beta 91 base pairs and 166 stacking pairs defined. Time for finding SS restraints: 25.30 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 removed outlier: 5.582A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 4.003A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.621A pdb=" N THR A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.632A pdb=" N ALA A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 479 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.575A pdb=" N SER A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 646 through 663 removed outlier: 6.148A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 671 through 692 removed outlier: 4.471A pdb=" N ILE A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A 690 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 750 through 769 removed outlier: 4.560A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 795 removed outlier: 3.504A pdb=" N ALA A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 834 Processing helix chain 'A' and resid 843 through 869 Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 924 removed outlier: 4.088A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 959 Processing helix chain 'A' and resid 986 through 1006 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.561A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1110 through 1126 removed outlier: 3.568A pdb=" N PHE A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1217 through 1232 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1272 through 1275 Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1329 through 1345 removed outlier: 3.640A pdb=" N SER A1341 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1352 Processing helix chain 'A' and resid 1354 through 1373 Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1412 through 1416 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1470 Processing helix chain 'A' and resid 1481 through 1483 No H-bonds generated for 'chain 'A' and resid 1481 through 1483' Processing helix chain 'A' and resid 1491 through 1495 Processing helix chain 'A' and resid 1497 through 1504 removed outlier: 4.694A pdb=" N HIS A1500 " --> pdb=" O ARG A1497 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1503 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 5.170A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 3.542A pdb=" N GLN A1548 " --> pdb=" O ASP A1545 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A1549 " --> pdb=" O VAL A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 3.811A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1586 Processing helix chain 'A' and resid 1592 through 1609 removed outlier: 3.514A pdb=" N THR A1596 " --> pdb=" O HIS A1592 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A1597 " --> pdb=" O ALA A1593 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1598 " --> pdb=" O GLN A1594 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A1599 " --> pdb=" O ARG A1595 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN A1600 " --> pdb=" O THR A1596 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A1601 " --> pdb=" O GLY A1597 " (cutoff:3.500A) Proline residue: A1602 - end of helix removed outlier: 4.339A pdb=" N ARG A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A1607 " --> pdb=" O ASN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 3.538A pdb=" N SER A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1668 Processing helix chain 'A' and resid 1674 through 1676 No H-bonds generated for 'chain 'A' and resid 1674 through 1676' Processing helix chain 'A' and resid 1724 through 1726 No H-bonds generated for 'chain 'A' and resid 1724 through 1726' Processing helix chain 'A' and resid 1748 through 1760 Processing helix chain 'A' and resid 1794 through 1808 Processing helix chain 'A' and resid 1810 through 1823 removed outlier: 3.916A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1844 Processing helix chain 'A' and resid 1896 through 1899 Processing helix chain 'A' and resid 1906 through 1923 Processing helix chain 'A' and resid 1938 through 1948 removed outlier: 4.724A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix removed outlier: 3.545A pdb=" N VAL A1946 " --> pdb=" O PRO A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1970 No H-bonds generated for 'chain 'A' and resid 1968 through 1970' Processing helix chain 'A' and resid 1972 through 1980 removed outlier: 3.537A pdb=" N LYS A1980 " --> pdb=" O ASP A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2016 Processing helix chain 'A' and resid 2019 through 2027 Processing helix chain 'A' and resid 2045 through 2066 removed outlier: 4.198A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2084 Processing helix chain 'C' and resid 120 through 128 removed outlier: 4.071A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 183 through 186 No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.109A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.842A pdb=" N ILE C 274 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 338 through 347 removed outlier: 4.464A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 345 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.897A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.619A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 588' Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix removed outlier: 4.366A pdb=" N ASN C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 785 through 804 removed outlier: 3.708A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 853 removed outlier: 4.176A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 4.031A pdb=" N THR C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA C 853 " --> pdb=" O GLY C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 883 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 909 through 911 No H-bonds generated for 'chain 'C' and resid 909 through 911' Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.710A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 53 through 64 Processing helix chain 'G' and resid 83 through 102 removed outlier: 3.580A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 104 through 109 removed outlier: 4.054A pdb=" N SER G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 174 removed outlier: 3.654A pdb=" N VAL G 117 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU G 128 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Proline residue: G 133 - end of helix removed outlier: 3.740A pdb=" N ARG G 148 " --> pdb=" O ASN G 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU G 155 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 165 Proline residue: H 161 - end of helix Processing helix chain 'H' and resid 173 through 182 Processing helix chain 'H' and resid 187 through 200 Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 237 through 249 Processing helix chain 'H' and resid 255 through 266 Proline residue: H 262 - end of helix Processing helix chain 'H' and resid 270 through 281 removed outlier: 3.609A pdb=" N ALA H 276 " --> pdb=" O PHE H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 302 through 314 Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 338 through 350 Processing helix chain 'H' and resid 356 through 365 removed outlier: 3.584A pdb=" N GLU H 363 " --> pdb=" O LYS H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 381 Processing helix chain 'H' and resid 388 through 397 Processing helix chain 'H' and resid 404 through 414 Processing helix chain 'H' and resid 423 through 436 Processing helix chain 'H' and resid 441 through 458 removed outlier: 4.253A pdb=" N TYR H 457 " --> pdb=" O TYR H 453 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP H 458 " --> pdb=" O GLY H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 482 Proline residue: H 477 - end of helix Processing helix chain 'H' and resid 488 through 500 Processing helix chain 'H' and resid 508 through 523 Proline residue: H 515 - end of helix Proline residue: H 518 - end of helix Processing helix chain 'H' and resid 528 through 541 Proline residue: H 533 - end of helix Processing helix chain 'H' and resid 547 through 559 removed outlier: 4.178A pdb=" N CYS H 556 " --> pdb=" O GLU H 553 " (cutoff:3.500A) Proline residue: H 557 - end of helix Processing helix chain 'H' and resid 570 through 578 removed outlier: 4.379A pdb=" N VAL H 577 " --> pdb=" O ALA H 573 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 578 " --> pdb=" O TYR H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 597 Processing helix chain 'H' and resid 602 through 635 Proline residue: H 613 - end of helix Proline residue: H 616 - end of helix removed outlier: 4.278A pdb=" N ILE H 619 " --> pdb=" O PHE H 615 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR H 621 " --> pdb=" O PRO H 617 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU H 622 " --> pdb=" O GLU H 618 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU H 626 " --> pdb=" O GLU H 622 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 635 " --> pdb=" O ALA H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 652 Processing helix chain 'H' and resid 664 through 675 removed outlier: 4.046A pdb=" N ARG H 675 " --> pdb=" O VAL H 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 688 Processing helix chain 'H' and resid 707 through 719 Processing helix chain 'H' and resid 723 through 733 removed outlier: 3.723A pdb=" N GLU H 727 " --> pdb=" O SER H 723 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN H 730 " --> pdb=" O ARG H 726 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU H 731 " --> pdb=" O GLU H 727 " (cutoff:3.500A) Processing helix chain 'H' and resid 741 through 755 removed outlier: 4.293A pdb=" N PHE H 751 " --> pdb=" O LYS H 747 " (cutoff:3.500A) Processing helix chain 'H' and resid 763 through 772 Processing helix chain 'H' and resid 780 through 791 Processing helix chain 'H' and resid 798 through 817 Processing helix chain 'I' and resid 40 through 60 removed outlier: 3.649A pdb=" N LYS I 50 " --> pdb=" O TYR I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'I' and resid 99 through 110 removed outlier: 4.015A pdb=" N GLU I 109 " --> pdb=" O TYR I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 removed outlier: 4.060A pdb=" N MET I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 144 Processing helix chain 'I' and resid 149 through 161 Processing helix chain 'I' and resid 166 through 178 removed outlier: 4.108A pdb=" N ARG I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 195 removed outlier: 3.857A pdb=" N ARG I 186 " --> pdb=" O TRP I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 212 Processing helix chain 'I' and resid 215 through 231 removed outlier: 3.808A pdb=" N THR I 228 " --> pdb=" O LEU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 235 No H-bonds generated for 'chain 'I' and resid 233 through 235' Processing helix chain 'I' and resid 240 through 257 Processing helix chain 'I' and resid 260 through 273 Processing helix chain 'I' and resid 298 through 310 Processing helix chain 'I' and resid 317 through 332 Processing helix chain 'I' and resid 341 through 353 Proline residue: I 351 - end of helix Processing helix chain 'I' and resid 361 through 368 removed outlier: 3.813A pdb=" N LEU I 366 " --> pdb=" O ARG I 362 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP I 367 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET I 368 " --> pdb=" O ILE I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 388 Processing helix chain 'I' and resid 394 through 400 Processing helix chain 'I' and resid 413 through 423 removed outlier: 3.950A pdb=" N ASP I 418 " --> pdb=" O LEU I 414 " (cutoff:3.500A) Proline residue: I 421 - end of helix Processing helix chain 'I' and resid 430 through 443 Proline residue: I 435 - end of helix removed outlier: 3.501A pdb=" N TYR I 443 " --> pdb=" O THR I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 462 Processing helix chain 'I' and resid 471 through 479 removed outlier: 3.549A pdb=" N GLU I 479 " --> pdb=" O SER I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 497 removed outlier: 3.670A pdb=" N TYR I 494 " --> pdb=" O VAL I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 515 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 539 through 550 Proline residue: I 545 - end of helix Processing helix chain 'I' and resid 561 through 575 removed outlier: 3.691A pdb=" N VAL I 575 " --> pdb=" O GLN I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 585 through 594 Processing helix chain 'I' and resid 602 through 619 Processing helix chain 'J' and resid 15 through 28 Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.604A pdb=" N TRP J 33 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER J 34 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA J 37 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU J 39 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 54 Processing helix chain 'J' and resid 67 through 79 Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 95 through 107 Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 165 through 193 Processing helix chain 'J' and resid 233 through 251 removed outlier: 4.356A pdb=" N ARG J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 355 removed outlier: 3.785A pdb=" N GLY J 355 " --> pdb=" O ASN J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 363 Processing helix chain 'J' and resid 374 through 381 Processing helix chain 'J' and resid 387 through 400 Processing helix chain 'J' and resid 425 through 437 Proline residue: J 432 - end of helix Processing helix chain 'J' and resid 445 through 468 removed outlier: 3.503A pdb=" N ALA J 450 " --> pdb=" O ASN J 446 " (cutoff:3.500A) Proline residue: J 467 - end of helix Processing helix chain 'J' and resid 483 through 586 removed outlier: 3.596A pdb=" N HIS J 487 " --> pdb=" O SER J 483 " (cutoff:3.500A) Proline residue: J 504 - end of helix removed outlier: 4.515A pdb=" N SER J 515 " --> pdb=" O GLU J 511 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS J 516 " --> pdb=" O SER J 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS J 526 " --> pdb=" O GLN J 522 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 527 " --> pdb=" O LEU J 523 " (cutoff:3.500A) Proline residue: J 532 - end of helix removed outlier: 3.689A pdb=" N GLN J 536 " --> pdb=" O PRO J 532 " (cutoff:3.500A) Proline residue: J 550 - end of helix removed outlier: 3.965A pdb=" N ILE J 553 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU J 554 " --> pdb=" O PRO J 550 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN J 556 " --> pdb=" O LEU J 552 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG J 557 " --> pdb=" O ILE J 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER J 572 " --> pdb=" O GLN J 568 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG J 577 " --> pdb=" O LEU J 573 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS J 578 " --> pdb=" O GLU J 574 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG J 579 " --> pdb=" O GLY J 575 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 580 " --> pdb=" O ARG J 576 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU J 584 " --> pdb=" O LEU J 580 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN J 585 " --> pdb=" O GLN J 581 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER J 586 " --> pdb=" O ALA J 582 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 121 Processing helix chain 'K' and resid 161 through 189 Processing helix chain 'K' and resid 198 through 210 Processing helix chain 'L' and resid 15 through 33 Proline residue: L 21 - end of helix removed outlier: 3.534A pdb=" N ASP L 25 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 67 removed outlier: 3.816A pdb=" N ILE L 52 " --> pdb=" O GLN L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 84 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 99 through 102 removed outlier: 4.524A pdb=" N LYS L 102 " --> pdb=" O GLY L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 102' Processing helix chain 'L' and resid 126 through 136 removed outlier: 4.463A pdb=" N GLU L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 62 removed outlier: 4.096A pdb=" N LYS T 61 " --> pdb=" O LYS T 57 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 395 No H-bonds generated for 'chain 'T' and resid 393 through 395' Processing helix chain 'M' and resid 4 through 7 No H-bonds generated for 'chain 'M' and resid 4 through 7' Processing helix chain 'M' and resid 64 through 67 No H-bonds generated for 'chain 'M' and resid 64 through 67' Processing helix chain 'M' and resid 84 through 93 removed outlier: 4.182A pdb=" N HIS M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 115 removed outlier: 4.009A pdb=" N LEU M 115 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 125 removed outlier: 3.955A pdb=" N ILE M 125 " --> pdb=" O GLY M 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 121 through 125' Processing helix chain 'M' and resid 216 through 226 Processing helix chain 'M' and resid 256 through 263 removed outlier: 4.237A pdb=" N ARG M 261 " --> pdb=" O LEU M 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 74 through 77 No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'N' and resid 84 through 86 No H-bonds generated for 'chain 'N' and resid 84 through 86' Processing helix chain 'N' and resid 96 through 104 removed outlier: 4.975A pdb=" N LEU N 104 " --> pdb=" O GLY N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 145 Processing helix chain 'N' and resid 153 through 167 removed outlier: 4.086A pdb=" N ARG N 166 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU N 167 " --> pdb=" O VAL N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 189 through 199 Processing helix chain 'N' and resid 212 through 217 removed outlier: 4.151A pdb=" N ARG N 216 " --> pdb=" O ASP N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 260 removed outlier: 4.242A pdb=" N VAL N 251 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS N 252 " --> pdb=" O ASN N 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 119 removed outlier: 3.534A pdb=" N LEU O 118 " --> pdb=" O ARG O 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU O 119 " --> pdb=" O TYR O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 397 through 399 No H-bonds generated for 'chain 'O' and resid 397 through 399' Processing helix chain 'P' and resid 14 through 18 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'Q' and resid 31 through 34 No H-bonds generated for 'chain 'Q' and resid 31 through 34' Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 63 through 84 removed outlier: 4.105A pdb=" N ALA Q 68 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 93 No H-bonds generated for 'chain 'Q' and resid 91 through 93' Processing helix chain 'Q' and resid 159 through 163 Processing helix chain 'Q' and resid 182 through 185 No H-bonds generated for 'chain 'Q' and resid 182 through 185' Processing helix chain 'Q' and resid 200 through 243 Processing helix chain 'S' and resid 287 through 300 Processing helix chain 'S' and resid 308 through 315 Processing helix chain 'S' and resid 324 through 335 Processing helix chain 'S' and resid 341 through 353 removed outlier: 4.160A pdb=" N PHE S 353 " --> pdb=" O ARG S 349 " (cutoff:3.500A) Processing helix chain 'S' and resid 355 through 370 Processing helix chain 'S' and resid 372 through 375 Processing helix chain 'S' and resid 380 through 393 removed outlier: 4.423A pdb=" N GLY S 385 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS S 386 " --> pdb=" O ILE S 383 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP S 388 " --> pdb=" O GLY S 385 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS S 390 " --> pdb=" O PHE S 387 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER S 393 " --> pdb=" O HIS S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 399 through 402 Processing helix chain 'S' and resid 414 through 431 removed outlier: 4.187A pdb=" N ASN S 429 " --> pdb=" O GLN S 425 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 441 Processing helix chain 'S' and resid 455 through 467 Processing helix chain 'S' and resid 475 through 484 Processing helix chain 'U' and resid 81 through 87 removed outlier: 3.930A pdb=" N ILE U 85 " --> pdb=" O GLN U 82 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA U 86 " --> pdb=" O GLU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 99 No H-bonds generated for 'chain 'U' and resid 97 through 99' Processing helix chain 'U' and resid 106 through 130 removed outlier: 5.389A pdb=" N GLU U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA U 130 " --> pdb=" O ALA U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 133 through 152 removed outlier: 4.704A pdb=" N LEU U 137 " --> pdb=" O PRO U 133 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP U 138 " --> pdb=" O GLU U 134 " (cutoff:3.500A) Proline residue: U 145 - end of helix Processing helix chain 'U' and resid 157 through 171 Processing helix chain 'U' and resid 173 through 188 removed outlier: 3.585A pdb=" N ILE U 176 " --> pdb=" O PRO U 173 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN U 177 " --> pdb=" O LYS U 174 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 245 removed outlier: 3.554A pdb=" N SER U 232 " --> pdb=" O LEU U 228 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS U 234 " --> pdb=" O ILE U 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG U 235 " --> pdb=" O THR U 231 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 256 No H-bonds generated for 'chain 'V' and resid 254 through 256' Processing helix chain 'V' and resid 296 through 299 No H-bonds generated for 'chain 'V' and resid 296 through 299' Processing helix chain 'V' and resid 305 through 319 Processing helix chain 'V' and resid 333 through 341 Processing helix chain 'W' and resid 293 through 304 removed outlier: 3.553A pdb=" N TRP W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 312 No H-bonds generated for 'chain 'W' and resid 310 through 312' Processing helix chain 'W' and resid 440 through 444 Processing helix chain 'W' and resid 454 through 462 Processing helix chain 'W' and resid 476 through 482 removed outlier: 4.991A pdb=" N GLN W 481 " --> pdb=" O ALA W 478 " (cutoff:3.500A) Processing helix chain 'W' and resid 484 through 498 removed outlier: 5.896A pdb=" N SER W 490 " --> pdb=" O ALA W 487 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU W 492 " --> pdb=" O ARG W 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA W 495 " --> pdb=" O LEU W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 508 through 510 No H-bonds generated for 'chain 'W' and resid 508 through 510' Processing helix chain 'W' and resid 514 through 524 removed outlier: 3.722A pdb=" N GLN W 518 " --> pdb=" O THR W 514 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 552 Processing helix chain 'W' and resid 581 through 590 Processing helix chain 'W' and resid 610 through 625 removed outlier: 3.561A pdb=" N ILE W 624 " --> pdb=" O LYS W 620 " (cutoff:3.500A) Processing helix chain 'W' and resid 643 through 646 No H-bonds generated for 'chain 'W' and resid 643 through 646' Processing helix chain 'W' and resid 674 through 688 Processing helix chain 'W' and resid 701 through 720 removed outlier: 4.069A pdb=" N ASP W 720 " --> pdb=" O LYS W 716 " (cutoff:3.500A) Processing helix chain 'W' and resid 736 through 743 removed outlier: 3.553A pdb=" N ILE W 742 " --> pdb=" O ILE W 738 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE W 743 " --> pdb=" O GLN W 739 " (cutoff:3.500A) Processing helix chain 'W' and resid 758 through 762 removed outlier: 3.989A pdb=" N THR W 762 " --> pdb=" O ILE W 759 " (cutoff:3.500A) Processing helix chain 'W' and resid 799 through 810 removed outlier: 4.053A pdb=" N ALA W 809 " --> pdb=" O ARG W 805 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY W 810 " --> pdb=" O LYS W 806 " (cutoff:3.500A) Processing helix chain 'W' and resid 823 through 828 Processing helix chain 'W' and resid 837 through 840 Processing helix chain 'W' and resid 844 through 853 Processing helix chain 'W' and resid 858 through 860 No H-bonds generated for 'chain 'W' and resid 858 through 860' Processing helix chain 'W' and resid 869 through 881 Processing helix chain 'W' and resid 893 through 900 Processing helix chain 'W' and resid 905 through 917 removed outlier: 4.476A pdb=" N VAL W 915 " --> pdb=" O LEU W 911 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP W 916 " --> pdb=" O LEU W 912 " (cutoff:3.500A) Processing helix chain 'W' and resid 920 through 931 Processing helix chain 'W' and resid 943 through 953 removed outlier: 3.750A pdb=" N PHE W 953 " --> pdb=" O LYS W 949 " (cutoff:3.500A) Processing helix chain 'W' and resid 959 through 971 Processing helix chain 'W' and resid 976 through 983 Processing helix chain 'W' and resid 987 through 1007 Processing helix chain 'W' and resid 1017 through 1029 Processing helix chain 'W' and resid 1088 through 1094 Processing helix chain 'W' and resid 1101 through 1103 No H-bonds generated for 'chain 'W' and resid 1101 through 1103' Processing helix chain 'a' and resid 13 through 15 No H-bonds generated for 'chain 'a' and resid 13 through 15' Processing helix chain 'b' and resid 13 through 23 Processing helix chain 'b' and resid 84 through 86 No H-bonds generated for 'chain 'b' and resid 84 through 86' Processing helix chain 'c' and resid 15 through 21 Processing helix chain 'c' and resid 75 through 77 No H-bonds generated for 'chain 'c' and resid 75 through 77' Processing helix chain 'e' and resid 6 through 14 Processing helix chain 'f' and resid 3 through 9 Processing helix chain 'f' and resid 103 through 107 Processing helix chain 'g' and resid 16 through 28 Processing helix chain 'g' and resid 32 through 40 Processing helix chain 'h' and resid 13 through 15 No H-bonds generated for 'chain 'h' and resid 13 through 15' Processing helix chain 'i' and resid 13 through 23 Processing helix chain 'i' and resid 84 through 86 No H-bonds generated for 'chain 'i' and resid 84 through 86' Processing helix chain 'j' and resid 15 through 21 Processing helix chain 'j' and resid 75 through 77 No H-bonds generated for 'chain 'j' and resid 75 through 77' Processing helix chain 'l' and resid 6 through 14 Processing helix chain 'm' and resid 3 through 9 Processing helix chain 'm' and resid 103 through 107 Processing helix chain 'o' and resid 5 through 10 removed outlier: 3.512A pdb=" N ASP o 10 " --> pdb=" O SER o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 47 through 50 Processing helix chain 'o' and resid 111 through 119 removed outlier: 4.607A pdb=" N ARG o 116 " --> pdb=" O ASP o 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG o 119 " --> pdb=" O ARG o 116 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 136 Processing helix chain 'o' and resid 140 through 147 Processing helix chain 'p' and resid 41 through 55 removed outlier: 4.195A pdb=" N THR p 54 " --> pdb=" O LEU p 50 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE p 55 " --> pdb=" O LEU p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 88 Processing helix chain 'q' and resid 25 through 34 Processing helix chain 'q' and resid 78 through 142 removed outlier: 3.656A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS q 108 " --> pdb=" O SER q 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS q 135 " --> pdb=" O ASN q 131 " (cutoff:3.500A) Proline residue: q 138 - end of helix Processing helix chain 'r' and resid 25 through 34 Processing helix chain 'r' and resid 78 through 138 removed outlier: 3.718A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU r 93 " --> pdb=" O ASP r 89 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG r 99 " --> pdb=" O ASN r 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR r 101 " --> pdb=" O LYS r 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU r 115 " --> pdb=" O THR r 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS r 120 " --> pdb=" O ARG r 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Proline residue: r 138 - end of helix Processing helix chain 's' and resid 25 through 34 removed outlier: 3.724A pdb=" N GLN s 30 " --> pdb=" O SER s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 139 removed outlier: 3.723A pdb=" N LEU s 93 " --> pdb=" O ASP s 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE s 96 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU s 98 " --> pdb=" O GLU s 94 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR s 101 " --> pdb=" O LYS s 97 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER s 104 " --> pdb=" O SER s 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS s 107 " --> pdb=" O ASP s 103 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU s 121 " --> pdb=" O ASP s 117 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN s 131 " --> pdb=" O LEU s 127 " (cutoff:3.500A) Proline residue: s 138 - end of helix Processing helix chain 't' and resid 25 through 34 removed outlier: 3.589A pdb=" N LYS t 33 " --> pdb=" O GLU t 29 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 141 removed outlier: 3.594A pdb=" N GLU t 94 " --> pdb=" O ALA t 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET t 128 " --> pdb=" O ALA t 124 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN t 131 " --> pdb=" O LEU t 127 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU t 132 " --> pdb=" O MET t 128 " (cutoff:3.500A) Proline residue: t 138 - end of helix removed outlier: 3.648A pdb=" N SER t 141 " --> pdb=" O LEU t 137 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 970 through 973 Processing sheet with id= D, first strand: chain 'A' and resid 1247 through 1251 removed outlier: 3.770A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= F, first strand: chain 'A' and resid 1258 through 1262 removed outlier: 6.875A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id= H, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= I, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= J, first strand: chain 'A' and resid 1734 through 1738 removed outlier: 6.330A pdb=" N VAL A1773 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLN A1737 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A1775 " --> pdb=" O GLN A1737 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1986 through 1989 removed outlier: 4.034A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 7.569A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 320 through 322 removed outlier: 9.449A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ILE C 134 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET C 209 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 136 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN C 211 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 138 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 213 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLY C 140 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.318A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.618A pdb=" N LYS C 474 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= Q, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= R, first strand: chain 'C' and resid 710 through 714 removed outlier: 6.839A pdb=" N VAL C 773 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU C 820 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE C 775 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER C 767 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 927 through 929 removed outlier: 7.104A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 143 through 145 Processing sheet with id= U, first strand: chain 'T' and resid 186 through 190 removed outlier: 3.639A pdb=" N ALA T 167 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'T' and resid 209 through 214 removed outlier: 6.797A pdb=" N SER T 224 " --> pdb=" O LYS T 210 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU T 212 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU T 222 " --> pdb=" O LEU T 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE T 214 " --> pdb=" O SER T 220 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N SER T 220 " --> pdb=" O PHE T 214 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP T 234 " --> pdb=" O VAL T 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL T 240 " --> pdb=" O ASP T 234 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'T' and resid 253 through 255 Processing sheet with id= X, first strand: chain 'T' and resid 296 through 300 removed outlier: 6.804A pdb=" N SER T 311 " --> pdb=" O LEU T 297 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU T 299 " --> pdb=" O ILE T 309 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE T 309 " --> pdb=" O LEU T 299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS T 329 " --> pdb=" O ILE T 319 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU T 321 " --> pdb=" O PRO T 327 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'T' and resid 342 through 344 removed outlier: 3.639A pdb=" N ARG T 359 " --> pdb=" O SER T 355 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'T' and resid 389 through 391 removed outlier: 6.024A pdb=" N ASP T 411 " --> pdb=" O LEU T 417 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU T 417 " --> pdb=" O ASP T 411 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 241 through 243 Processing sheet with id= AB, first strand: chain 'N' and resid 222 through 225 removed outlier: 3.884A pdb=" N CYS N 181 " --> pdb=" O VAL N 176 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 145 through 147 Processing sheet with id= AD, first strand: chain 'O' and resid 260 through 262 removed outlier: 3.542A pdb=" N ILE O 260 " --> pdb=" O LEU O 250 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 269 through 274 removed outlier: 6.832A pdb=" N SER O 284 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL O 272 " --> pdb=" O VAL O 282 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL O 282 " --> pdb=" O VAL O 272 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER O 285 " --> pdb=" O THR O 289 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR O 289 " --> pdb=" O SER O 285 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'O' and resid 314 through 316 Processing sheet with id= AG, first strand: chain 'O' and resid 353 through 358 removed outlier: 6.602A pdb=" N GLY O 367 " --> pdb=" O ASN O 354 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU O 356 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE O 365 " --> pdb=" O LEU O 356 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE O 358 " --> pdb=" O VAL O 363 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL O 363 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 404 through 407 removed outlier: 4.143A pdb=" N CYS O 404 " --> pdb=" O GLY O 417 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY O 417 " --> pdb=" O CYS O 404 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 164 through 167 Processing sheet with id= AJ, first strand: chain 'O' and resid 185 through 190 removed outlier: 6.952A pdb=" N VAL O 200 " --> pdb=" O ARG O 186 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL O 188 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE O 198 " --> pdb=" O VAL O 188 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'W' and resid 652 through 654 removed outlier: 8.918A pdb=" N ILE W 653 " --> pdb=" O PHE W 501 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL W 503 " --> pdb=" O ILE W 653 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL W 631 " --> pdb=" O LEU W 502 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE W 504 " --> pdb=" O VAL W 631 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL W 633 " --> pdb=" O ILE W 504 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET W 530 " --> pdb=" O SER W 598 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE W 600 " --> pdb=" O MET W 530 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY W 532 " --> pdb=" O ILE W 600 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU W 602 " --> pdb=" O GLY W 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR W 534 " --> pdb=" O LEU W 602 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 662 through 666 removed outlier: 6.456A pdb=" N GLY W 815 " --> pdb=" O GLU W 663 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU W 665 " --> pdb=" O GLY W 815 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS W 817 " --> pdb=" O LEU W 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'W' and resid 726 through 730 removed outlier: 6.365A pdb=" N ILE W 694 " --> pdb=" O VAL W 754 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA W 756 " --> pdb=" O ILE W 694 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL W 696 " --> pdb=" O ALA W 756 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU W 695 " --> pdb=" O TYR W 770 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL W 772 " --> pdb=" O LEU W 695 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE W 697 " --> pdb=" O VAL W 772 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 777 through 784 Processing sheet with id= AO, first strand: chain 'W' and resid 1033 through 1035 Processing sheet with id= AP, first strand: chain 'W' and resid 1071 through 1074 Processing sheet with id= AQ, first strand: chain 'a' and resid 77 through 83 removed outlier: 6.282A pdb=" N CYS a 48 " --> pdb=" O LEU a 82 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'a' and resid 43 through 45 Processing sheet with id= AS, first strand: chain 'b' and resid 58 through 61 removed outlier: 3.543A pdb=" N GLN b 34 " --> pdb=" O LEU b 31 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU b 31 " --> pdb=" O GLN b 34 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N GLY b 36 " --> pdb=" O ILE b 29 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE b 29 " --> pdb=" O GLY b 36 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N ARG b 38 " --> pdb=" O VAL b 27 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL b 27 " --> pdb=" O ARG b 38 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'b' and resid 52 through 54 removed outlier: 3.846A pdb=" N VAL b 52 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU b 82 " --> pdb=" O VAL b 52 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 37 through 39 removed outlier: 7.116A pdb=" N GLU c 58 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR c 67 " --> pdb=" O GLU c 58 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'c' and resid 71 through 73 removed outlier: 3.636A pdb=" N GLN c 52 " --> pdb=" O SER c 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER c 44 " --> pdb=" O GLN c 52 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN c 54 " --> pdb=" O LEU c 42 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU c 42 " --> pdb=" O ASN c 54 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'c' and resid 28 through 31 removed outlier: 4.001A pdb=" N TYR c 80 " --> pdb=" O LYS c 30 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'd' and resid 23 through 25 Processing sheet with id= AY, first strand: chain 'd' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP d 41 " --> pdb=" O LEU d 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU d 29 " --> pdb=" O ASP d 41 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'e' and resid 69 through 73 removed outlier: 6.949A pdb=" N GLU e 22 " --> pdb=" O LYS e 70 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE e 72 " --> pdb=" O SER e 20 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER e 20 " --> pdb=" O ILE e 72 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN e 43 " --> pdb=" O VAL e 34 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'e' and resid 47 through 50 Processing sheet with id= BB, first strand: chain 'f' and resid 80 through 82 removed outlier: 3.705A pdb=" N GLU f 13 " --> pdb=" O LEU f 29 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'f' and resid 84 through 87 removed outlier: 6.501A pdb=" N THR f 41 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU f 29 " --> pdb=" O THR f 41 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 87 through 91 removed outlier: 3.576A pdb=" N ARG g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'g' and resid 67 through 70 Processing sheet with id= BF, first strand: chain 'h' and resid 77 through 83 removed outlier: 6.282A pdb=" N CYS h 48 " --> pdb=" O LEU h 82 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'h' and resid 43 through 45 Processing sheet with id= BH, first strand: chain 'i' and resid 58 through 61 removed outlier: 3.545A pdb=" N GLN i 34 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU i 31 " --> pdb=" O GLN i 34 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY i 36 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N ILE i 29 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ARG i 38 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL i 27 " --> pdb=" O ARG i 38 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'i' and resid 52 through 54 removed outlier: 3.845A pdb=" N VAL i 52 " --> pdb=" O LEU i 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU i 82 " --> pdb=" O VAL i 52 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'j' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU j 58 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR j 67 " --> pdb=" O GLU j 58 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 71 through 73 removed outlier: 3.637A pdb=" N GLN j 52 " --> pdb=" O SER j 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER j 44 " --> pdb=" O GLN j 52 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN j 54 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU j 42 " --> pdb=" O ASN j 54 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'j' and resid 28 through 31 removed outlier: 4.003A pdb=" N TYR j 80 " --> pdb=" O LYS j 30 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 23 through 25 Processing sheet with id= BN, first strand: chain 'k' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP k 41 " --> pdb=" O LEU k 29 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU k 29 " --> pdb=" O ASP k 41 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'l' and resid 69 through 73 removed outlier: 6.949A pdb=" N GLU l 22 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER l 20 " --> pdb=" O ILE l 72 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN l 43 " --> pdb=" O VAL l 34 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'l' and resid 47 through 50 Processing sheet with id= BQ, first strand: chain 'm' and resid 80 through 82 removed outlier: 3.707A pdb=" N GLU m 13 " --> pdb=" O LEU m 29 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'm' and resid 84 through 87 removed outlier: 6.500A pdb=" N THR m 41 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU m 29 " --> pdb=" O THR m 41 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'n' and resid 53 through 55 removed outlier: 3.578A pdb=" N ARG n 89 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'n' and resid 67 through 70 Processing sheet with id= BU, first strand: chain 'n' and resid 45 through 48 removed outlier: 3.636A pdb=" N VAL n 103 " --> pdb=" O SER n 47 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'o' and resid 13 through 15 removed outlier: 7.108A pdb=" N ILE o 56 " --> pdb=" O LEU o 36 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR o 78 " --> pdb=" O LEU o 57 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN o 100 " --> pdb=" O LEU o 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN o 126 " --> pdb=" O LEU o 101 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'p' and resid 72 through 74 Processing sheet with id= BX, first strand: chain 'q' and resid 13 through 15 Processing sheet with id= BY, first strand: chain 'r' and resid 13 through 16 removed outlier: 4.188A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 's' and resid 13 through 15 Processing sheet with id= CA, first strand: chain 't' and resid 13 through 15 2945 hydrogen bonds defined for protein. 8130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 394 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 42.05 Time building geometry restraints manager: 28.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 11883 1.29 - 1.44: 22555 1.44 - 1.59: 42672 1.59 - 1.73: 718 1.73 - 1.88: 413 Bond restraints: 78241 Sorted by residual: bond pdb=" CB HIS T 185 " pdb=" CG HIS T 185 " ideal model delta sigma weight residual 1.497 1.828 -0.331 1.40e-02 5.10e+03 5.58e+02 bond pdb=" CA LEU V 302 " pdb=" CB LEU V 302 " ideal model delta sigma weight residual 1.530 1.289 0.241 1.69e-02 3.50e+03 2.04e+02 bond pdb=" CB CYS T 444 " pdb=" SG CYS T 444 " ideal model delta sigma weight residual 1.808 1.429 0.379 3.30e-02 9.18e+02 1.32e+02 bond pdb=" CA ASP o 69 " pdb=" CB ASP o 69 " ideal model delta sigma weight residual 1.532 1.381 0.151 1.42e-02 4.96e+03 1.12e+02 bond pdb=" CD ARG A 716 " pdb=" NE ARG A 716 " ideal model delta sigma weight residual 1.458 1.317 0.141 1.40e-02 5.10e+03 1.01e+02 ... (remaining 78236 not shown) Histogram of bond angle deviations from ideal: 77.83 - 93.54: 11 93.54 - 109.25: 13898 109.25 - 124.96: 90711 124.96 - 140.66: 2908 140.66 - 156.37: 1 Bond angle restraints: 107529 Sorted by residual: angle pdb=" C LYS T 152 " pdb=" CA LYS T 152 " pdb=" CB LYS T 152 " ideal model delta sigma weight residual 111.23 77.83 33.40 1.42e+00 4.96e-01 5.53e+02 angle pdb=" N TYR T 130 " pdb=" CA TYR T 130 " pdb=" C TYR T 130 " ideal model delta sigma weight residual 109.81 156.37 -46.56 2.21e+00 2.05e-01 4.44e+02 angle pdb=" N PRO o 44 " pdb=" CA PRO o 44 " pdb=" CB PRO o 44 " ideal model delta sigma weight residual 103.23 113.86 -10.63 6.70e-01 2.23e+00 2.52e+02 angle pdb=" N LYS T 153 " pdb=" CA LYS T 153 " pdb=" CB LYS T 153 " ideal model delta sigma weight residual 110.49 133.71 -23.22 1.69e+00 3.50e-01 1.89e+02 angle pdb=" N PRO T 424 " pdb=" CA PRO T 424 " pdb=" CB PRO T 424 " ideal model delta sigma weight residual 103.25 116.05 -12.80 1.05e+00 9.07e-01 1.49e+02 ... (remaining 107524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 46243 35.23 - 70.46: 1619 70.46 - 105.68: 156 105.68 - 140.91: 37 140.91 - 176.14: 19 Dihedral angle restraints: 48074 sinusoidal: 21530 harmonic: 26544 Sorted by residual: dihedral pdb=" CA ALA e 81 " pdb=" C ALA e 81 " pdb=" N PRO e 82 " pdb=" CA PRO e 82 " ideal model delta harmonic sigma weight residual -180.00 -52.74 -127.26 0 5.00e+00 4.00e-02 6.48e+02 dihedral pdb=" CA ALA l 81 " pdb=" C ALA l 81 " pdb=" N PRO l 82 " pdb=" CA PRO l 82 " ideal model delta harmonic sigma weight residual -180.00 -52.81 -127.19 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA PHE A 239 " pdb=" C PHE A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta harmonic sigma weight residual -180.00 -54.24 -125.76 0 5.00e+00 4.00e-02 6.33e+02 ... (remaining 48071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 12689 1.014 - 2.028: 1 2.028 - 3.042: 0 3.042 - 4.056: 0 4.056 - 5.069: 2 Chirality restraints: 12692 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.42e+02 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 2.54 -4.87 2.00e-01 2.50e+01 5.94e+02 chirality pdb=" CA TYR T 130 " pdb=" N TYR T 130 " pdb=" C TYR T 130 " pdb=" CB TYR T 130 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.89e+01 ... (remaining 12689 not shown) Planarity restraints: 12347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W1064 " 0.263 2.00e-02 2.50e+03 1.40e-01 3.94e+02 pdb=" CG TYR W1064 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR W1064 " -0.128 2.00e-02 2.50e+03 pdb=" CD2 TYR W1064 " -0.133 2.00e-02 2.50e+03 pdb=" CE1 TYR W1064 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR W1064 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR W1064 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR W1064 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR W 666 " -0.173 2.00e-02 2.50e+03 1.04e-01 2.15e+02 pdb=" CG TYR W 666 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR W 666 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR W 666 " 0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR W 666 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR W 666 " 0.066 2.00e-02 2.50e+03 pdb=" CZ TYR W 666 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR W 666 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR W 967 " 0.194 2.00e-02 2.50e+03 1.02e-01 2.07e+02 pdb=" CG TYR W 967 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR W 967 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR W 967 " -0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR W 967 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR W 967 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR W 967 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR W 967 " 0.139 2.00e-02 2.50e+03 ... (remaining 12344 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 192 2.24 - 2.91: 33918 2.91 - 3.57: 111319 3.57 - 4.24: 179051 4.24 - 4.90: 284471 Nonbonded interactions: 608951 Sorted by model distance: nonbonded pdb=" NH2 ARG A2056 " pdb=" O ALA V 331 " model vdw 1.581 2.520 nonbonded pdb=" O LEU T 129 " pdb=" CD2 HIS T 176 " model vdw 1.602 3.260 nonbonded pdb=" O3' G E -1 " pdb=" P U E 351 " model vdw 1.616 3.400 nonbonded pdb=" P G E 1 " pdb=" O2' A E 301 " model vdw 1.633 3.400 nonbonded pdb=" C2 A D 40 " pdb=" NE ARG N 121 " model vdw 1.736 3.420 ... (remaining 608946 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 6 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 102)) selection = chain 'h' } ncs_group { reference = chain 'b' selection = chain 'i' } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = chain 'd' selection = chain 'k' } ncs_group { reference = (chain 'e' and resid 4 through 84) selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'q' and (resid 1 through 52 or resid 57 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 139)) selection = (chain 'r' and (resid 1 through 52 or resid 60 or resid 65 through 139)) selection = (chain 's' and (resid 1 through 52 or resid 57 or resid 65 through 139)) selection = (chain 't' and (resid 1 through 52 or resid 57 or resid 65 through 139)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.060 Extract box with map and model: 15.630 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 194.840 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 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 : 0.013 0.379 78241 Z= 0.868 Angle : 1.684 46.558 107529 Z= 1.058 Chirality : 0.114 5.069 12692 Planarity : 0.012 0.318 12347 Dihedral : 17.762 176.140 30734 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 2.03 % Allowed : 11.60 % Favored : 86.37 % Rotamer: Outliers : 4.17 % Allowed : 6.47 % Favored : 89.36 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.61 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.07), residues: 8803 helix: -3.09 (0.06), residues: 3898 sheet: -2.49 (0.13), residues: 1064 loop : -3.09 (0.08), residues: 3841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.008 TRP A 711 HIS 0.022 0.004 HIS P 171 PHE 0.101 0.007 PHE W1029 TYR 0.263 0.010 TYR W1064 ARG 0.061 0.002 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17606 Ramachandran restraints generated. 8803 Oldfield, 0 Emsley, 8803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17606 Ramachandran restraints generated. 8803 Oldfield, 0 Emsley, 8803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1846 residues out of total 8229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1541 time to evaluate : 5.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable