Starting phenix.real_space_refine on Sat Mar 16 07:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y88_6817/03_2024/5y88_6817_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 345 5.49 5 Mg 6 5.21 5 S 209 5.16 5 C 44350 2.51 5 N 12783 2.21 5 O 14648 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 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" 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 GLU 757": "OE1" <-> "OE2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A GLU 1185": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1478": "OE1" <-> "OE2" Residue "A GLU 1479": "OE1" <-> "OE2" Residue "A GLU 1481": "OE1" <-> "OE2" 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 PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "C TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 996": "OE1" <-> "OE2" Residue "C GLU 1003": "OE1" <-> "OE2" Residue "H GLU 609": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "L ARG 151": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "N TYR 138": "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 TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 218": "OE1" <-> "OE2" Residue "R GLU 167": "OE1" <-> "OE2" Residue "R ARG 187": "NH1" <-> "NH2" Residue "R GLU 198": "OE1" <-> "OE2" Residue "R GLU 209": "OE1" <-> "OE2" Residue "S GLU 55": "OE1" <-> "OE2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "T GLU 98": "OE1" <-> "OE2" Residue "T ARG 99": "NH1" <-> "NH2" Residue "T ARG 134": "NH1" <-> "NH2" Residue "V GLU 207": "OE1" <-> "OE2" Residue "V GLU 233": "OE1" <-> "OE2" Residue "V GLU 241": "OE1" <-> "OE2" Residue "V GLU 243": "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 "q GLU 129": "OE1" <-> "OE2" Residue "q GLU 132": "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 "r GLU 132": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 29": "OE1" <-> "OE2" Residue "s GLU 48": "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" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72347 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 15715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1903, 15715 Classifications: {'peptide': 1903} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 99, 'TRANS': 1803} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 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: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7278 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 860} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2150 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 44, 'rna3p_pyr': 35} Link IDs: {'rna2p': 22, 'rna3p': 78} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 587 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 18} Chain breaks: 1 Chain: "F" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1727 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 15, 'rna3p_pur': 28, 'rna3p_pyr': 33} Link IDs: {'rna2p': 21, 'rna3p': 60} Chain breaks: 2 Chain: "G" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 921 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 308 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: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 3204 Classifications: {'peptide': 601} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 425} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 35 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1853 Unresolved non-hydrogen angles: 2399 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 164 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 32, 'TYR:plan': 28, 'ASN:plan1': 22, 'TRP:plan': 12, 'HIS:plan': 10, 'PHE:plan': 21, 'GLU:plan': 56, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 1044 Chain: "I" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3542 Classifications: {'peptide': 541} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 271} Link IDs: {'PTRANS': 13, 'TRANS': 527} Chain breaks: 20 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1149 Unresolved non-hydrogen angles: 1475 Unresolved non-hydrogen dihedrals: 984 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 19, 'ASN:plan1': 8, 'TRP:plan': 8, 'ASP:plan': 20, 'PHE:plan': 17, 'GLU:plan': 34, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 681 Chain: "J" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2944 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 8 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 619 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 499 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': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 368 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Chain: "L" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1290 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "M" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1298 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 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: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 554 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} 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: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 379 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 45} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 195 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "T" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "U" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 2690 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 384} Link IDs: {'PTRANS': 15, 'TRANS': 472} Chain breaks: 22 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1410 Unresolved non-hydrogen angles: 1797 Unresolved non-hydrogen dihedrals: 1176 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 26, 'TYR:plan': 17, 'ASN:plan1': 17, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 17, 'GLU:plan': 42, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 761 Chain: "V" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 619 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "W" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 3505 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 626} Link IDs: {'PTRANS': 36, 'TRANS': 671} Chain breaks: 2 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2308 Unresolved non-hydrogen angles: 2947 Unresolved non-hydrogen dihedrals: 1911 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 19, 'TYR:plan': 30, 'ASN:plan1': 27, 'TRP:plan': 3, 'ASP:plan': 45, 'PHE:plan': 28, 'GLU:plan': 57, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1288 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: "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: 200 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: 118 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: "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: 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: "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: "q" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 831 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 116 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': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "r" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 849 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 24 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: "s" 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: "t" 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: "x" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 177 Classifications: {'RNA': 9} Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 5} 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 42243 SG CYS L 104 56.392 183.067 118.502 1.00 74.29 S ATOM 42249 SG CYS L 105 59.693 184.971 119.133 1.00 85.35 S ATOM 42274 SG CYS L 108 59.687 181.639 117.202 1.00 56.35 S ATOM 42588 SG CYS L 148 59.429 181.851 120.346 1.00 58.43 S ATOM 42243 SG CYS L 104 56.392 183.067 118.502 1.00 74.29 S ATOM 42377 SG CYS L 122 56.640 179.784 116.676 1.00 55.92 S ATOM 42598 SG CYS L 150 53.390 180.901 117.924 1.00 96.80 S ATOM 42619 SG CYS L 153 55.099 182.825 115.409 1.00 63.15 S ATOM 42274 SG CYS L 108 59.687 181.639 117.202 1.00 56.35 S ATOM 42363 SG CYS L 120 60.208 178.198 116.044 1.00 69.23 S ATOM 42377 SG CYS L 122 56.640 179.784 116.676 1.00 55.92 S ATOM 42565 SG CYS L 145 59.030 178.641 119.359 1.00 45.74 S ATOM 42730 SG CYS M 13 64.843 146.743 117.649 1.00113.76 S ATOM 43188 SG CYS M 71 68.230 146.282 119.197 1.00100.06 S ATOM 43203 SG CYS M 73 66.794 149.330 119.896 1.00121.35 S ATOM 43209 SG CYS M 74 64.858 146.324 121.120 1.00 81.28 S ATOM 42888 SG CYS M 34 79.082 149.195 126.345 1.00 62.59 S ATOM 42911 SG CYS M 37 82.655 148.992 127.621 1.00 76.26 S ATOM 43110 SG CYS M 61 81.658 149.411 123.978 1.00 94.35 S ATOM 43134 SG CYS M 64 80.999 146.152 125.973 1.00 63.57 S ATOM 44525 SG CYS N 73 54.915 163.392 137.818 1.00 58.46 S ATOM 44587 SG CYS N 81 53.385 166.722 138.698 1.00 57.94 S ATOM 44627 SG CYS N 87 53.516 165.492 135.120 1.00 55.65 S Time building chain proxies: 33.29, per 1000 atoms: 0.46 Number of scatterers: 72347 At special positions: 0 Unit cell: (241.61, 270.342, 297.768, 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 209 16.00 P 345 15.00 Mg 6 11.99 O 14648 8.00 N 12783 7.00 C 44350 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: 24.74 Conformation dependent library (CDL) restraints added in 9.6 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 153 " 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 150 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " 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 71 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 73 " pdb="ZN ZN M 400 " - pdb=" SG CYS M 13 " pdb=" ZN M 401 " 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 ZN M 401 " - pdb=" SG CYS M 37 " 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=" SG CYS N 87 " pdb="ZN ZN N 400 " - pdb=" NE2 HIS N 91 " Number of angles added : 33 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 333 helices and 72 sheets defined 46.9% alpha, 9.8% beta 78 base pairs and 147 stacking pairs defined. Time for finding SS restraints: 28.47 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 removed outlier: 5.268A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 4.692A pdb=" N THR A 156 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.551A pdb=" N LYS A 174 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 305 through 318 removed outlier: 4.174A 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 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' 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 473 through 479 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.794A pdb=" N ARG A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' 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 551 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 640 Processing helix chain 'A' and resid 647 through 663 removed outlier: 6.250A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.098A 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: 3.654A pdb=" N ILE A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 689 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 690 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 735 removed outlier: 3.632A pdb=" N ILE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.611A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 794 Processing helix chain 'A' and resid 806 through 836 removed outlier: 4.041A pdb=" N ARG A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 870 removed outlier: 4.022A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 908 through 924 removed outlier: 4.351A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 3.633A pdb=" N ILE A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1005 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.887A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.798A 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 1108 through 1126 removed outlier: 4.227A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A1113 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A1123 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1126 " --> pdb=" O LEU A1123 " (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 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1328 through 1346 Processing helix chain 'A' and resid 1349 through 1352 Processing helix chain 'A' and resid 1354 through 1357 No H-bonds generated for 'chain 'A' and resid 1354 through 1357' Processing helix chain 'A' and resid 1360 through 1372 Processing helix chain 'A' and resid 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' Processing helix chain 'A' and resid 1392 through 1394 No H-bonds generated for 'chain 'A' and resid 1392 through 1394' Processing helix chain 'A' and resid 1409 through 1412 removed outlier: 3.535A pdb=" N LEU A1412 " --> pdb=" O ALA A1409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1409 through 1412' Processing helix chain 'A' and resid 1440 through 1443 No H-bonds generated for 'chain 'A' and resid 1440 through 1443' Processing helix chain 'A' and resid 1447 through 1470 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 4.271A pdb=" N GLY A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A1483 " --> pdb=" O GLU A1479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1483' Processing helix chain 'A' and resid 1491 through 1495 Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 4.736A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 4.442A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 Processing helix chain 'A' and resid 1553 through 1559 removed outlier: 4.029A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1609 Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 4.404A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1673 through 1676 No H-bonds generated for 'chain 'A' and resid 1673 through 1676' Processing helix chain 'A' and resid 1748 through 1761 Processing helix chain 'A' and resid 1794 through 1808 removed outlier: 3.890A pdb=" N ASN A1800 " --> pdb=" O PRO A1796 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1823 removed outlier: 3.807A 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 1901 removed outlier: 4.300A pdb=" N GLY A1901 " --> pdb=" O VAL A1898 " (cutoff:3.500A) Processing helix chain 'A' and resid 1905 through 1923 Processing helix chain 'A' and resid 1941 through 1950 removed outlier: 3.930A pdb=" N LEU A1949 " --> pdb=" O GLU A1945 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP A1950 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1970 removed outlier: 4.449A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2020 through 2027 Processing helix chain 'A' and resid 2045 through 2067 removed outlier: 3.870A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2076 through 2084 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.777A pdb=" N MET C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.583A pdb=" N LEU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 170' Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.747A pdb=" N VAL C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.587A pdb=" N TYR C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) 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: 4.757A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.910A 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 402 removed outlier: 3.834A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.380A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' 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 587 removed outlier: 3.823A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 587' Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix removed outlier: 4.239A pdb=" N LEU C 619 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 626 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 759 through 764 removed outlier: 3.906A pdb=" N ARG C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 785 through 804 removed outlier: 3.990A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 851 removed outlier: 3.990A pdb=" N ILE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 870 through 883 Proline residue: C 874 - end of helix 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 973 removed outlier: 3.756A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 993 Processing helix chain 'C' and resid 995 through 1003 removed outlier: 3.596A pdb=" N GLN C1000 " --> pdb=" O GLU C 996 " (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: 3.581A 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: 4.052A pdb=" N SER G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 174 removed outlier: 3.656A 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: 3.741A 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: 3.852A pdb=" N ARG G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 119 Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 141 through 150 removed outlier: 3.607A pdb=" N LYS H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) Proline residue: H 150 - end of helix Processing helix chain 'H' and resid 157 through 167 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 217 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 280 removed outlier: 3.607A 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 364 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 405 through 414 Processing helix chain 'H' and resid 422 through 436 Processing helix chain 'H' and resid 441 through 458 removed outlier: 4.254A pdb=" N TYR H 457 " --> pdb=" O TYR H 453 " (cutoff:3.500A) removed outlier: 3.867A 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 509 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: 4.177A 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: 3.736A 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 634 Proline residue: H 613 - end of helix Proline residue: H 616 - end of helix removed outlier: 4.276A pdb=" N ILE H 619 " --> pdb=" O PHE H 615 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR H 621 " --> pdb=" O PRO H 617 " (cutoff:3.500A) removed outlier: 3.853A 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) Processing helix chain 'H' and resid 641 through 652 Processing helix chain 'H' and resid 664 through 675 removed outlier: 4.047A pdb=" N ARG H 675 " --> pdb=" O VAL H 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 681 through 688 Processing helix chain 'H' and resid 707 through 719 Processing helix chain 'H' and resid 723 through 733 removed outlier: 3.722A 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: 4.291A pdb=" N PHE H 751 " --> pdb=" O LYS H 747 " (cutoff:3.500A) Processing helix chain 'H' and resid 762 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: 3.701A pdb=" N GLU I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.720A 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 111 removed outlier: 3.884A pdb=" N GLU I 109 " --> pdb=" O TYR I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 removed outlier: 3.745A pdb=" N MET I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER I 127 " --> pdb=" O ASN I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 146 removed outlier: 3.852A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 161 Processing helix chain 'I' and resid 166 through 178 removed outlier: 3.868A pdb=" N ARG I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 195 removed outlier: 3.747A pdb=" N ARG I 186 " --> pdb=" O TRP I 182 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU I 187 " --> pdb=" O ASN I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 212 removed outlier: 3.502A pdb=" N GLU I 209 " --> pdb=" O TRP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 235 removed outlier: 3.612A pdb=" N ILE I 226 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR I 228 " --> pdb=" O LEU I 224 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN I 234 " --> pdb=" O ALA I 230 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU I 235 " --> pdb=" O ASN I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 256 Processing helix chain 'I' and resid 260 through 272 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: 3.814A pdb=" N LEU I 366 " --> pdb=" O ARG I 362 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP I 367 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET I 368 " --> pdb=" O ILE I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 381 through 388 Processing helix chain 'I' and resid 394 through 400 Processing helix chain 'I' and resid 413 through 423 removed outlier: 3.951A 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: 3.502A 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 469 through 479 removed outlier: 3.676A pdb=" N ILE I 473 " --> pdb=" O SER I 469 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU I 479 " --> pdb=" O SER I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 497 removed outlier: 3.671A 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: 3.693A 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 'I' and resid 626 through 640 Proline residue: I 639 - end of helix Processing helix chain 'J' and resid 15 through 28 Processing helix chain 'J' and resid 33 through 39 removed outlier: 3.507A pdb=" N SER J 38 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU J 39 " --> pdb=" O LYS J 35 " (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 86 through 91 Processing helix chain 'J' and resid 95 through 106 Processing helix chain 'J' and resid 146 through 159 Processing helix chain 'J' and resid 165 through 193 Processing helix chain 'J' and resid 233 through 248 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 388 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: 3.506A 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: 4.514A 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: 3.702A 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: 3.688A 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: 3.540A 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: 3.676A pdb=" N ARG J 557 " --> pdb=" O ILE J 553 " (cutoff:3.500A) removed outlier: 3.509A 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: 4.491A pdb=" N LYS J 578 " --> pdb=" O GLU J 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG J 579 " --> pdb=" O GLY J 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU J 580 " --> pdb=" O ARG J 576 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU J 584 " --> pdb=" O LEU J 580 " (cutoff:3.500A) removed outlier: 4.046A 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 97 through 122 removed outlier: 3.565A pdb=" N ALA K 101 " --> pdb=" O TYR K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 189 removed outlier: 5.873A pdb=" N LYS K 163 " --> pdb=" O LYS K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 210 Processing helix chain 'L' and resid 14 through 33 removed outlier: 4.120A pdb=" N GLU L 17 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.744A pdb=" N ASP L 25 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 68 removed outlier: 3.618A 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 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 126 through 136 removed outlier: 3.745A pdb=" N GLU L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) 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 63 through 66 No H-bonds generated for 'chain 'M' and resid 63 through 66' Processing helix chain 'M' and resid 84 through 93 removed outlier: 4.176A pdb=" N HIS M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 115 removed outlier: 4.523A pdb=" N LEU M 115 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 removed outlier: 3.579A pdb=" N ASP M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 274 Proline residue: M 273 - end of helix Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 55 through 58 No H-bonds generated for 'chain 'N' and resid 55 through 58' 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: 5.331A 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: 4.416A pdb=" N ARG N 166 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 4.204A 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 210 through 217 removed outlier: 4.696A pdb=" N ASP N 213 " --> pdb=" O LYS N 210 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG N 216 " --> pdb=" O ASP N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 260 removed outlier: 3.627A pdb=" N VAL N 251 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS N 252 " --> pdb=" O ASN N 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 117 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 19 Processing helix chain 'P' and resid 164 through 173 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 82 removed outlier: 3.843A pdb=" N ALA Q 68 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 92 No H-bonds generated for 'chain 'Q' and resid 90 through 92' 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 199 through 246 removed outlier: 3.536A pdb=" N LEU Q 208 " --> pdb=" O LEU Q 204 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Q 218 " --> pdb=" O LYS Q 214 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS Q 226 " --> pdb=" O LYS Q 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU Q 241 " --> pdb=" O LYS Q 237 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN Q 246 " --> pdb=" O LYS Q 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'S' and resid 53 through 62 removed outlier: 4.031A pdb=" N LYS S 61 " --> pdb=" O LYS S 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR S 62 " --> pdb=" O ARG S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 19 No H-bonds generated for 'chain 'T' and resid 16 through 19' Processing helix chain 'T' and resid 35 through 48 Processing helix chain 'T' and resid 63 through 74 Processing helix chain 'T' and resid 77 through 85 Proline residue: T 81 - end of helix Processing helix chain 'T' and resid 93 through 113 removed outlier: 3.610A pdb=" N SER T 111 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER T 112 " --> pdb=" O GLU T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 139 Processing helix chain 'U' and resid 85 through 128 Proline residue: U 90 - end of helix Proline residue: U 97 - end of helix removed outlier: 3.869A pdb=" N PHE U 106 " --> pdb=" O GLY U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 153 Processing helix chain 'U' and resid 160 through 177 Proline residue: U 173 - end of helix Processing helix chain 'U' and resid 186 through 202 Processing helix chain 'U' and resid 208 through 227 Proline residue: U 217 - end of helix Processing helix chain 'U' and resid 233 through 252 removed outlier: 4.216A pdb=" N LEU U 248 " --> pdb=" O LYS U 244 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR U 249 " --> pdb=" O HIS U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 260 through 279 Processing helix chain 'U' and resid 286 through 305 Processing helix chain 'U' and resid 311 through 330 Proline residue: U 326 - end of helix Processing helix chain 'U' and resid 339 through 352 Processing helix chain 'U' and resid 357 through 367 Processing helix chain 'U' and resid 374 through 393 Proline residue: U 392 - end of helix Processing helix chain 'U' and resid 403 through 417 Processing helix chain 'U' and resid 426 through 442 Processing helix chain 'U' and resid 450 through 463 Proline residue: U 461 - end of helix Processing helix chain 'U' and resid 471 through 478 Processing helix chain 'U' and resid 487 through 502 Processing helix chain 'U' and resid 512 through 521 Processing helix chain 'U' and resid 529 through 539 Processing helix chain 'U' and resid 549 through 558 Processing helix chain 'U' and resid 564 through 573 Processing helix chain 'U' and resid 582 through 589 Processing helix chain 'U' and resid 633 through 644 removed outlier: 3.553A pdb=" N VAL U 637 " --> pdb=" O PHE U 633 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 233 Processing helix chain 'V' and resid 241 through 251 removed outlier: 3.574A pdb=" N GLN V 245 " --> pdb=" O GLU V 241 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY V 250 " --> pdb=" O LEU V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 303 removed outlier: 3.746A pdb=" N LEU V 289 " --> pdb=" O SER V 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG V 291 " --> pdb=" O ILE V 287 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS V 292 " --> pdb=" O CYS V 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 67 Processing helix chain 'W' and resid 81 through 92 removed outlier: 4.152A pdb=" N GLU W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 106 removed outlier: 5.348A pdb=" N ASP W 100 " --> pdb=" O ALA W 97 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 133 Proline residue: W 127 - end of helix Processing helix chain 'W' and resid 150 through 163 Processing helix chain 'W' and resid 193 through 202 Processing helix chain 'W' and resid 222 through 237 removed outlier: 3.936A pdb=" N GLN W 233 " --> pdb=" O GLY W 229 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS W 236 " --> pdb=" O LYS W 232 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 258 Processing helix chain 'W' and resid 286 through 299 Processing helix chain 'W' and resid 313 through 333 Processing helix chain 'W' and resid 350 through 357 removed outlier: 4.591A pdb=" N ILE W 356 " --> pdb=" O GLN W 352 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE W 357 " --> pdb=" O GLN W 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 418 through 427 Processing helix chain 'W' and resid 442 through 446 Processing helix chain 'W' and resid 465 through 472 Processing helix chain 'W' and resid 488 through 500 Processing helix chain 'W' and resid 512 through 517 Processing helix chain 'W' and resid 524 through 536 removed outlier: 4.580A pdb=" N PHE W 534 " --> pdb=" O LEU W 530 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU W 535 " --> pdb=" O ILE W 531 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE W 536 " --> pdb=" O GLY W 532 " (cutoff:3.500A) Processing helix chain 'W' and resid 539 through 549 Processing helix chain 'W' and resid 562 through 572 removed outlier: 4.026A pdb=" N PHE W 572 " --> pdb=" O ALA W 568 " (cutoff:3.500A) Processing helix chain 'W' and resid 578 through 589 Processing helix chain 'W' and resid 592 through 597 Processing helix chain 'W' and resid 600 through 603 No H-bonds generated for 'chain 'W' and resid 600 through 603' Processing helix chain 'W' and resid 610 through 629 Processing helix chain 'W' and resid 643 through 655 removed outlier: 3.897A pdb=" N GLY W 655 " --> pdb=" O ALA W 651 " (cutoff:3.500A) Processing helix chain 'W' and resid 715 through 721 Processing helix chain 'W' and resid 728 through 730 No H-bonds generated for 'chain 'W' and resid 728 through 730' Processing helix chain 'W' and resid 736 through 754 removed outlier: 3.795A pdb=" N LEU W 740 " --> pdb=" O VAL W 736 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE W 743 " --> pdb=" O SER W 739 " (cutoff:3.500A) 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 '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: 4.608A pdb=" N ARG o 116 " --> pdb=" O ASP o 113 " (cutoff:3.500A) removed outlier: 3.563A 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: 5.284A 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 '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 'q' and resid 25 through 34 removed outlier: 3.725A pdb=" N GLN q 30 " --> pdb=" O SER q 26 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 139 removed outlier: 3.723A pdb=" N LEU q 93 " --> pdb=" O ASP q 89 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE q 96 " --> pdb=" O MET q 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU q 98 " --> pdb=" O GLU q 94 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER q 104 " --> pdb=" O SER q 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS q 107 " --> pdb=" O ASP q 103 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU q 121 " --> pdb=" O ASP q 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN q 131 " --> pdb=" O LEU q 127 " (cutoff:3.500A) Proline residue: q 138 - end of helix Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.590A pdb=" N LYS r 33 " --> pdb=" O GLU r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 82 through 141 removed outlier: 3.594A pdb=" N GLU r 94 " --> pdb=" O ALA r 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET r 128 " --> pdb=" O ALA r 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN r 131 " --> pdb=" O LEU r 127 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU r 132 " --> pdb=" O MET r 128 " (cutoff:3.500A) Proline residue: r 138 - end of helix removed outlier: 3.648A pdb=" N SER r 141 " --> pdb=" O LEU r 137 " (cutoff:3.500A) Processing helix chain 's' and resid 25 through 34 Processing helix chain 's' and resid 78 through 142 removed outlier: 3.655A pdb=" N ALA s 90 " --> pdb=" O ASN s 86 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS s 97 " --> pdb=" O LEU s 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR s 101 " --> pdb=" O LYS s 97 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS s 108 " --> pdb=" O SER s 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA s 123 " --> pdb=" O ALA s 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET s 128 " --> pdb=" O ALA s 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS s 135 " --> pdb=" O ASN s 131 " (cutoff:3.500A) Proline residue: s 138 - end of helix Processing helix chain 't' and resid 25 through 34 Processing helix chain 't' and resid 78 through 138 removed outlier: 3.717A pdb=" N THR t 82 " --> pdb=" O PRO t 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU t 93 " --> pdb=" O ASP t 89 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU t 98 " --> pdb=" O GLU t 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG t 99 " --> pdb=" O ASN t 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR t 101 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU t 102 " --> pdb=" O LEU t 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU t 115 " --> pdb=" O THR t 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS t 120 " --> pdb=" O ARG t 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU t 121 " --> pdb=" O ASP t 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN t 125 " --> pdb=" O LEU t 121 " (cutoff:3.500A) Proline residue: t 138 - end of helix 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 1247 through 1252 removed outlier: 3.894A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= E, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.682A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1414 through 1418 Processing sheet with id= G, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= H, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= I, first strand: chain 'A' and resid 1734 through 1739 removed outlier: 6.849A pdb=" N VAL A1773 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN A1737 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A1775 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG A1739 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A1777 " --> pdb=" O ARG A1739 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1985 through 1990 removed outlier: 3.521A pdb=" N GLN A1985 " --> pdb=" O ILE A1893 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1859 through 1863 removed outlier: 4.062A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 320 through 322 removed outlier: 9.227A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 536 through 538 removed outlier: 6.563A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 668 through 670 removed outlier: 3.525A pdb=" N HIS C 642 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 677 through 681 Processing sheet with id= P, first strand: chain 'C' and resid 774 through 776 removed outlier: 8.124A pdb=" N ILE C 775 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR C 818 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 928 through 931 removed outlier: 3.658A pdb=" N TYR C 931 " --> pdb=" O GLU C 863 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU C 899 " --> pdb=" O VAL C 894 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 894 " --> pdb=" O LEU C 899 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 249 through 252 Processing sheet with id= S, first strand: chain 'N' and resid 222 through 225 removed outlier: 4.023A pdb=" N CYS N 181 " --> pdb=" O VAL N 176 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 145 through 147 Processing sheet with id= U, first strand: chain 'O' and resid 227 through 232 removed outlier: 6.455A pdb=" N ALA O 242 " --> pdb=" O ARG O 228 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL O 230 " --> pdb=" O ALA O 240 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA O 240 " --> pdb=" O VAL O 230 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE O 232 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU O 238 " --> pdb=" O ILE O 232 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP O 252 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 269 through 274 removed outlier: 6.857A pdb=" N SER O 284 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL O 272 " --> pdb=" O VAL O 282 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL O 282 " --> pdb=" O VAL O 272 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 314 through 316 Processing sheet with id= X, first strand: chain 'O' and resid 353 through 358 removed outlier: 6.662A pdb=" N GLY O 367 " --> pdb=" O ASN O 354 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU O 356 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE O 365 " --> pdb=" O LEU O 356 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE O 358 " --> pdb=" O VAL O 363 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL O 363 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 413 through 418 removed outlier: 3.836A pdb=" N SER O 422 " --> pdb=" O GLU O 418 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 164 through 167 removed outlier: 3.564A pdb=" N THR O 176 " --> pdb=" O VAL O 166 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 185 through 190 removed outlier: 7.074A pdb=" N VAL O 200 " --> pdb=" O ARG O 186 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL O 188 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE O 198 " --> pdb=" O VAL O 188 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'U' and resid 647 through 649 removed outlier: 3.534A pdb=" N MET U 680 " --> pdb=" O ILE U 673 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'U' and resid 655 through 659 Processing sheet with id= AD, first strand: chain 'U' and resid 689 through 692 removed outlier: 4.283A pdb=" N LEU U 689 " --> pdb=" O ILE U 701 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'W' and resid 263 through 267 removed outlier: 6.614A pdb=" N ILE W 243 " --> pdb=" O MET W 112 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE W 114 " --> pdb=" O ILE W 243 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE W 245 " --> pdb=" O PHE W 114 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY W 116 " --> pdb=" O ILE W 245 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER W 247 " --> pdb=" O GLY W 116 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLN W 142 " --> pdb=" O SER W 210 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE W 212 " --> pdb=" O GLN W 142 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA W 144 " --> pdb=" O ILE W 212 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU W 214 " --> pdb=" O ALA W 144 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR W 146 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR W 192 " --> pdb=" O SER W 175 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'W' and resid 274 through 278 removed outlier: 6.926A pdb=" N GLY W 434 " --> pdb=" O GLU W 275 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR W 277 " --> pdb=" O GLY W 434 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS W 436 " --> pdb=" O TYR W 277 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP W 305 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL W 391 " --> pdb=" O ASP W 305 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU W 307 " --> pdb=" O VAL W 391 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP W 393 " --> pdb=" O LEU W 307 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE W 309 " --> pdb=" O ASP W 393 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 396 through 403 Processing sheet with id= AH, first strand: chain 'W' and resid 670 through 672 Processing sheet with id= AI, first strand: chain 'W' and resid 698 through 701 Processing sheet with id= AJ, first strand: chain 'a' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS a 48 " --> pdb=" O LEU a 82 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 43 through 45 Processing sheet with id= AL, 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: 4.336A pdb=" N LEU b 31 " --> pdb=" O GLN b 34 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY b 36 " --> pdb=" O ILE b 29 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N ILE b 29 " --> pdb=" O GLY b 36 " (cutoff:3.500A) removed outlier: 10.100A 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= AM, first strand: chain 'b' and resid 52 through 54 removed outlier: 3.847A pdb=" N VAL b 52 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 82 " --> pdb=" O VAL b 52 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'c' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU c 58 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR c 67 " --> pdb=" O GLU c 58 " (cutoff:3.500A) Processing sheet with id= AO, 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: 3.690A pdb=" N SER c 44 " --> pdb=" O GLN c 52 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN c 54 " --> pdb=" O LEU c 42 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU c 42 " --> pdb=" O ASN c 54 " (cutoff:3.500A) Processing sheet with id= AP, 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= AQ, first strand: chain 'd' and resid 23 through 25 Processing sheet with id= AR, first strand: chain 'd' and resid 60 through 63 removed outlier: 6.048A pdb=" N ASP d 41 " --> pdb=" O LEU d 29 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU d 29 " --> pdb=" O ASP d 41 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'e' and resid 69 through 73 removed outlier: 6.948A 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: 6.530A pdb=" N GLN e 43 " --> pdb=" O VAL e 34 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'e' and resid 47 through 50 Processing sheet with id= AU, 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= AV, first strand: chain 'f' and resid 84 through 87 removed outlier: 6.500A 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= AW, first strand: chain 'g' and resid 87 through 91 removed outlier: 3.577A 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= AX, first strand: chain 'g' and resid 67 through 70 Processing sheet with id= AY, first strand: chain 'o' and resid 13 through 15 removed outlier: 7.107A pdb=" N ILE o 56 " --> pdb=" O LEU o 36 " (cutoff:3.500A) removed outlier: 6.612A 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: 6.548A pdb=" N ASN o 126 " --> pdb=" O LEU o 101 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'p' and resid 72 through 74 Processing sheet with id= BA, first strand: chain 'h' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS h 48 " --> pdb=" O LEU h 82 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 43 through 45 Processing sheet with id= BC, first strand: chain 'i' and resid 58 through 61 removed outlier: 3.544A 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: 9.740A pdb=" N GLY i 36 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N ILE i 29 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 10.099A 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= BD, first strand: chain 'i' and resid 52 through 54 removed outlier: 3.846A pdb=" N VAL i 52 " --> pdb=" O LEU i 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU i 82 " --> pdb=" O VAL i 52 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'j' and resid 37 through 39 removed outlier: 7.119A pdb=" N GLU j 58 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR j 67 " --> pdb=" O GLU j 58 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'j' and resid 71 through 73 removed outlier: 3.638A pdb=" N GLN j 52 " --> pdb=" O SER j 44 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER j 44 " --> pdb=" O GLN j 52 " (cutoff:3.500A) removed outlier: 6.118A 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= BG, 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= BH, first strand: chain 'k' and resid 23 through 25 Processing sheet with id= BI, 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= BJ, 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: 4.655A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.493A 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= BK, first strand: chain 'l' and resid 47 through 50 Processing sheet with id= BL, first strand: chain 'm' and resid 80 through 82 removed outlier: 3.706A pdb=" N GLU m 13 " --> pdb=" O LEU m 29 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'm' and resid 84 through 87 removed outlier: 6.501A pdb=" N THR m 41 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU m 29 " --> pdb=" O THR m 41 " (cutoff:3.500A) Processing sheet with id= BN, 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= BO, first strand: chain 'n' and resid 67 through 70 Processing sheet with id= BP, 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= BQ, first strand: chain 'q' and resid 13 through 15 Processing sheet with id= BR, first strand: chain 'r' and resid 13 through 15 Processing sheet with id= BS, first strand: chain 's' and resid 13 through 15 Processing sheet with id= BT, first strand: chain 't' and resid 13 through 16 removed outlier: 4.188A pdb=" N THR t 21 " --> pdb=" O SER t 16 " (cutoff:3.500A) 3173 hydrogen bonds defined for protein. 8931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 189 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 78 basepair parallelities 147 stacking parallelities Total time for adding SS restraints: 37.87 Time building geometry restraints manager: 27.04 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: 11555 1.29 - 1.43: 19284 1.43 - 1.56: 42146 1.56 - 1.70: 710 1.70 - 1.83: 347 Bond restraints: 74042 Sorted by residual: bond pdb=" N HIS C 934 " pdb=" CA HIS C 934 " ideal model delta sigma weight residual 1.459 1.322 0.136 1.28e-02 6.10e+03 1.13e+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 1.13e+02 bond pdb=" CA TRP C 933 " pdb=" C TRP C 933 " ideal model delta sigma weight residual 1.523 1.383 0.140 1.34e-02 5.57e+03 1.10e+02 bond pdb=" CB CYS H 712 " pdb=" SG CYS H 712 " ideal model delta sigma weight residual 1.808 1.527 0.281 3.30e-02 9.18e+02 7.25e+01 bond pdb=" CA ARG A1497 " pdb=" C ARG A1497 " ideal model delta sigma weight residual 1.523 1.632 -0.109 1.34e-02 5.57e+03 6.60e+01 ... (remaining 74037 not shown) Histogram of bond angle deviations from ideal: 85.94 - 97.07: 14 97.07 - 108.21: 6881 108.21 - 119.34: 57663 119.34 - 130.48: 36956 130.48 - 141.62: 380 Bond angle restraints: 101894 Sorted by residual: angle pdb=" CA LEU W 462 " pdb=" C LEU W 462 " pdb=" N SER W 463 " ideal model delta sigma weight residual 118.14 85.94 32.20 1.56e+00 4.11e-01 4.26e+02 angle pdb=" N PRO o 44 " pdb=" CA PRO o 44 " pdb=" CB PRO o 44 " ideal model delta sigma weight residual 103.23 113.94 -10.71 6.70e-01 2.23e+00 2.56e+02 angle pdb=" C ARG P 6 " pdb=" N PRO P 7 " pdb=" CA PRO P 7 " ideal model delta sigma weight residual 119.84 139.31 -19.47 1.25e+00 6.40e-01 2.43e+02 angle pdb=" C LEU W 462 " pdb=" N SER W 463 " pdb=" CA SER W 463 " ideal model delta sigma weight residual 121.54 94.29 27.25 1.91e+00 2.74e-01 2.03e+02 angle pdb=" O ILE U 440 " pdb=" C ILE U 440 " pdb=" N PHE U 441 " ideal model delta sigma weight residual 121.91 109.68 12.23 9.80e-01 1.04e+00 1.56e+02 ... (remaining 101889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 43766 35.83 - 71.65: 1470 71.65 - 107.48: 127 107.48 - 143.31: 35 143.31 - 179.13: 22 Dihedral angle restraints: 45420 sinusoidal: 18863 harmonic: 26557 Sorted by residual: dihedral pdb=" CA GLY O 351 " pdb=" C GLY O 351 " pdb=" N ILE O 352 " pdb=" CA ILE O 352 " ideal model delta harmonic sigma weight residual 180.00 48.39 131.61 0 5.00e+00 4.00e-02 6.93e+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 -49.02 -130.98 0 5.00e+00 4.00e-02 6.86e+02 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 -52.81 -127.19 0 5.00e+00 4.00e-02 6.47e+02 ... (remaining 45417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.994: 12231 0.994 - 1.988: 2 1.988 - 2.982: 0 2.982 - 3.976: 0 3.976 - 4.971: 2 Chirality restraints: 12235 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 2.45 -4.97 2.00e-01 2.50e+01 6.18e+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 2.48 -4.82 2.00e-01 2.50e+01 5.81e+02 chirality pdb=" CA ASN V 239 " pdb=" N ASN V 239 " pdb=" C ASN V 239 " pdb=" CB ASN V 239 " both_signs ideal model delta sigma weight residual False 2.51 0.72 1.79 2.00e-01 2.50e+01 8.02e+01 ... (remaining 12232 not shown) Planarity restraints: 11897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU W 462 " 0.067 2.00e-02 2.50e+03 1.74e-01 3.02e+02 pdb=" C LEU W 462 " -0.299 2.00e-02 2.50e+03 pdb=" O LEU W 462 " 0.132 2.00e-02 2.50e+03 pdb=" N SER W 463 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 478 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C LEU U 478 " 0.217 2.00e-02 2.50e+03 pdb=" O LEU U 478 " -0.080 2.00e-02 2.50e+03 pdb=" N GLU U 479 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU U 119 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C GLU U 119 " 0.216 2.00e-02 2.50e+03 pdb=" O GLU U 119 " -0.080 2.00e-02 2.50e+03 pdb=" N ASP U 120 " -0.069 2.00e-02 2.50e+03 ... (remaining 11894 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 28 1.87 - 2.63: 1570 2.63 - 3.38: 100328 3.38 - 4.14: 171152 4.14 - 4.90: 295929 Nonbonded interactions: 569007 Sorted by model distance: nonbonded pdb=" CB SER W 703 " pdb=" N3 U x 2 " model vdw 1.112 3.520 nonbonded pdb=" CG GLN A 662 " pdb=" CG1 VAL A1621 " model vdw 1.289 3.860 nonbonded pdb=" O SER C 682 " pdb=" O ALA C 853 " model vdw 1.328 3.040 nonbonded pdb=" OG SER A1415 " pdb=" NE2 HIS A1746 " model vdw 1.406 2.520 nonbonded pdb=" OE2 GLU A1364 " pdb=" OH TYR A1389 " model vdw 1.509 2.440 ... (remaining 569002 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' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'q' and (resid 1 through 51 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 'r' and (resid 1 through 51 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 's' and (resid 1 through 51 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 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 't' and (resid 1 through 51 or resid 57 through 61 or resid 65 through 13 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.140 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: 0.040 Extract box with map and model: 16.220 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 194.860 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 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 : 0.011 0.281 74042 Z= 0.733 Angle : 1.454 32.204 101894 Z= 0.983 Chirality : 0.106 4.971 12235 Planarity : 0.012 0.174 11897 Dihedral : 17.407 179.132 28022 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 1.19 % Allowed : 6.20 % Favored : 92.61 % Rotamer: Outliers : 5.35 % Allowed : 5.65 % Favored : 89.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.06 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.08), residues: 8774 helix: -1.61 (0.06), residues: 4251 sheet: -1.87 (0.14), residues: 1003 loop : -2.23 (0.09), residues: 3520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.007 TRP A 217 HIS 0.019 0.003 HIS A 389 PHE 0.055 0.005 PHE C 603 TYR 0.052 0.006 TYR I 267 ARG 0.034 0.002 ARG A1317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1874 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1545 time to evaluate : 5.910 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 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