Starting phenix.real_space_refine on Sun Mar 17 02:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wsg_6684/03_2024/5wsg_6684_updated.pdb" } resolution = 4.0 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 379 5.49 5 Mg 6 5.21 5 S 236 5.16 5 C 47113 2.51 5 N 13437 2.21 5 O 15553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1490": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 252": "NH1" <-> "NH2" Residue "Q ARG 261": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 42": "NH1" <-> "NH2" Residue "Z ARG 53": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 108": "NH1" <-> "NH2" Residue "Z ARG 149": "NH1" <-> "NH2" Residue "Z ARG 178": "NH1" <-> "NH2" Residue "Z ARG 191": "NH1" <-> "NH2" Residue "Z ARG 201": "NH1" <-> "NH2" Residue "Z ARG 382": "NH1" <-> "NH2" Residue "Z ARG 439": "NH1" <-> "NH2" Residue "c ARG 85": "NH1" <-> "NH2" Residue "v GLU 609": "OE1" <-> "OE2" Residue "n GLU 55": "OE1" <-> "OE2" Residue "n ARG 60": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o GLU 29": "OE1" <-> "OE2" Residue "o GLU 48": "OE1" <-> "OE2" Residue "o GLU 129": "OE1" <-> "OE2" Residue "o GLU 132": "OE1" <-> "OE2" Residue "p GLU 24": "OE1" <-> "OE2" Residue "p GLU 29": "OE1" <-> "OE2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "p GLU 94": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p GLU 132": "OE1" <-> "OE2" Residue "q GLU 24": "OE1" <-> "OE2" Residue "q GLU 29": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "r GLU 24": "OE1" <-> "OE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r GLU 48": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 129": "OE1" <-> "OE2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "j ARG 30": "NH1" <-> "NH2" Residue "m ARG 88": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ARG 97": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "f GLU 83": "OE1" <-> "OE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76730 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 15939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1931, 15939 Classifications: {'peptide': 1931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 99, 'TRANS': 1830} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7019 Classifications: {'peptide': 878} Link IDs: {'PTRANS': 49, 'TRANS': 828} Chain breaks: 2 Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2646 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 323} Chain: "P" 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: "Q" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1472 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 3 Chain: "R" 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: "S" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "Z" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3651 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 6} Chain: "N" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain: "D" 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: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 21, 'rna3p': 81} Chain: "L" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1909 Classifications: {'RNA': 91} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 17, 'rna3p_pur': 29, 'rna3p_pyr': 39} Link IDs: {'rna2p': 23, 'rna3p': 67} Chain breaks: 2 Chain: "M" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 486 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "c" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 2971 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 5, 'UNK:plan-1': 118, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 288 Chain: "d" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3506 Classifications: {'peptide': 532} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 283} Link IDs: {'PTRANS': 5, 'TRANS': 526} Chain breaks: 20 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 292} Unresolved non-hydrogen planarities: 292 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "v" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 3183 Classifications: {'peptide': 593} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 458} Link IDs: {'PTRANS': 6, 'TRANS': 586} Chain breaks: 32 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1166 Unresolved non-hydrogen angles: 1721 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 2, 'TYR:plan': 2, 'UNK:plan-1': 460, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 595 Chain: "n" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 1870 Classifications: {'peptide': 296} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 277} Chain breaks: 11 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 336 Chain: "o" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "p" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "q" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2345 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 1052 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 22, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 420 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "t" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 315 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: "k" 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: "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: "h" 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: "j" 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: "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: "F" 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: "G" 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: "H" 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: "U" 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: "V" 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: "W" 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: "X" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 513 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "Y" 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: "b" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 208 Classifications: {'DNA': 1, 'RNA': 13} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna3p': 13} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' A:plan': 1, ' A%rna3p_pur:plan2': 1, ' U%rna3p_pyr:plan': 6, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 85 Chain: "e" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 3360 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 604} Link IDs: {'PTRANS': 27, 'TRANS': 651} Chain breaks: 2 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 2129 Unresolved non-hydrogen angles: 2722 Unresolved non-hydrogen dihedrals: 1756 Unresolved non-hydrogen chiralities: 222 Planarities with less than four sites: {'GLN:plan1': 31, 'ARG:plan': 30, 'TYR:plan': 24, 'ASN:plan1': 26, 'TRP:plan': 5, 'HIS:plan': 12, 'PHE:plan': 31, 'GLU:plan': 32, 'ASP:plan': 42} Unresolved non-hydrogen planarities: 1065 Chain: "f" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1202 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain breaks: 1 Chain: "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: "Q" 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27462 SG CYS Q 13 71.706 143.566 123.380 1.00 0.00 S ATOM 27920 SG CYS Q 71 75.010 142.431 124.896 1.00 0.00 S ATOM 27935 SG CYS Q 73 73.056 145.072 126.419 1.00 0.00 S ATOM 27941 SG CYS Q 74 71.662 141.512 126.440 1.00 0.00 S ATOM 27620 SG CYS Q 34 85.492 145.909 132.214 1.00 0.00 S ATOM 27643 SG CYS Q 37 88.856 145.639 133.508 1.00 0.00 S ATOM 27842 SG CYS Q 61 88.123 146.171 129.869 1.00 0.00 S ATOM 27866 SG CYS Q 64 87.591 142.784 131.635 1.00 0.00 S ATOM 29431 SG CYS R 73 60.098 157.767 144.124 1.00 0.00 S ATOM 29493 SG CYS R 81 59.017 161.214 144.854 1.00 0.00 S ATOM 29533 SG CYS R 87 59.052 159.801 141.327 1.00 0.00 S ATOM 32386 SG CYS T 104 59.573 177.754 124.490 1.00 0.00 S ATOM 32392 SG CYS T 105 62.432 180.185 125.431 1.00 0.00 S ATOM 32417 SG CYS T 108 63.270 176.761 123.657 1.00 0.00 S ATOM 32731 SG CYS T 148 62.723 177.510 126.930 1.00 0.00 S ATOM 32386 SG CYS T 104 59.573 177.754 124.490 1.00 0.00 S ATOM 32520 SG CYS T 122 60.447 174.868 122.707 1.00 0.00 S ATOM 32741 SG CYS T 150 56.979 175.153 123.776 1.00 0.00 S ATOM 32762 SG CYS T 153 58.059 177.665 121.171 1.00 0.00 S ATOM 32417 SG CYS T 108 63.270 176.761 123.657 1.00 0.00 S ATOM 32506 SG CYS T 120 64.333 173.386 122.600 1.00 0.00 S ATOM 32520 SG CYS T 122 60.447 174.868 122.707 1.00 0.00 S ATOM 32708 SG CYS T 145 62.677 173.476 125.566 1.00 0.00 S Time building chain proxies: 29.97, per 1000 atoms: 0.39 Number of scatterers: 76730 At special positions: 0 Unit cell: (232.468, 304.298, 282.096, 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 236 16.00 P 379 15.00 Mg 6 11.99 O 15553 8.00 N 13437 7.00 C 47113 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: 26.38 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 73 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 64 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 61 " pdb=" ZN R 400 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 81 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 148 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 104 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 153 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " Number of angles added : 33 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 331 helices and 85 sheets defined 47.2% alpha, 12.0% beta 88 base pairs and 156 stacking pairs defined. Time for finding SS restraints: 26.70 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 removed outlier: 5.412A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.962A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 210 through 229 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.513A 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 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.614A pdb=" N ALA A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 479 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.723A pdb=" N SER A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 646 through 663 removed outlier: 5.931A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.884A 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 689 removed outlier: 4.484A pdb=" N ILE A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 748 through 769 removed outlier: 4.259A pdb=" N ASP A 751 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 752 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 759 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 760 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 766 " --> pdb=" O MET A 763 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 769 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 795 Processing helix chain 'A' and resid 806 through 834 Processing helix chain 'A' and resid 842 through 869 removed outlier: 3.823A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 924 removed outlier: 4.054A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 959 Processing helix chain 'A' and resid 986 through 1006 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.704A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.772A 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: 4.372A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A1113 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 4.240A 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 1217 through 1232 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1272 through 1275 No H-bonds generated for 'chain 'A' and resid 1272 through 1275' Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1329 through 1345 removed outlier: 3.682A pdb=" N SER A1341 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1352 Processing helix chain 'A' and resid 1354 through 1373 Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1412 through 1416 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1470 Processing helix chain 'A' and resid 1481 through 1483 No H-bonds generated for 'chain 'A' and resid 1481 through 1483' Processing helix chain 'A' and resid 1491 through 1495 Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 5.607A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 5.105A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 3.634A pdb=" N GLN A1548 " --> pdb=" O ASP A1545 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1549 " --> pdb=" O VAL A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 3.837A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1582 No H-bonds generated for 'chain 'A' and resid 1580 through 1582' Processing helix chain 'A' and resid 1592 through 1597 Processing helix chain 'A' and resid 1601 through 1609 removed outlier: 4.069A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A1608 " --> pdb=" O ARG A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1653 through 1668 Processing helix chain 'A' and resid 1674 through 1676 No H-bonds generated for 'chain 'A' and resid 1674 through 1676' Processing helix chain 'A' and resid 1724 through 1726 No H-bonds generated for 'chain 'A' and resid 1724 through 1726' Processing helix chain 'A' and resid 1748 through 1760 Processing helix chain 'A' and resid 1794 through 1808 Processing helix chain 'A' and resid 1810 through 1823 removed outlier: 3.927A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1844 Processing helix chain 'A' and resid 1896 through 1899 Processing helix chain 'A' and resid 1906 through 1923 Processing helix chain 'A' and resid 1938 through 1948 removed outlier: 4.639A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix Processing helix chain 'A' and resid 1968 through 1970 No H-bonds generated for 'chain 'A' and resid 1968 through 1970' Processing helix chain 'A' and resid 1972 through 1980 removed outlier: 3.516A pdb=" N LYS A1980 " --> pdb=" O ASP A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2016 Processing helix chain 'A' and resid 2019 through 2027 Processing helix chain 'A' and resid 2045 through 2066 removed outlier: 4.231A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2084 Processing helix chain 'C' and resid 120 through 128 removed outlier: 4.036A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.701A 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 183 through 186 No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 222 through 231 removed outlier: 4.146A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 338 through 347 removed outlier: 4.316A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 4.228A 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 404 removed outlier: 3.881A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.632A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 588' Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix removed outlier: 4.582A pdb=" N ASN C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 785 through 804 removed outlier: 3.848A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 853 removed outlier: 4.212A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 4.008A pdb=" N THR C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 853 " --> pdb=" O GLY C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 883 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 909 through 911 No H-bonds generated for 'chain 'C' and resid 909 through 911' Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.767A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 119 removed outlier: 3.508A pdb=" N LEU O 118 " --> pdb=" O ARG O 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 119 " --> pdb=" O TYR O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 397 through 399 No H-bonds generated for 'chain 'O' and resid 397 through 399' Processing helix chain 'P' and resid 31 through 34 No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 40 through 42 No H-bonds generated for 'chain 'P' and resid 40 through 42' Processing helix chain 'P' and resid 63 through 84 removed outlier: 4.074A pdb=" N ALA P 68 " --> pdb=" O GLN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 159 through 162 No H-bonds generated for 'chain 'P' and resid 159 through 162' Processing helix chain 'P' and resid 182 through 185 No H-bonds generated for 'chain 'P' and resid 182 through 185' Processing helix chain 'P' and resid 200 through 242 Processing helix chain 'Q' and resid 4 through 6 No H-bonds generated for 'chain 'Q' and resid 4 through 6' Processing helix chain 'Q' and resid 64 through 67 No H-bonds generated for 'chain 'Q' and resid 64 through 67' Processing helix chain 'Q' and resid 84 through 93 removed outlier: 4.148A pdb=" N HIS Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 115 removed outlier: 3.977A pdb=" N LEU Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 125 removed outlier: 4.094A pdb=" N ILE Q 125 " --> pdb=" O GLY Q 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 121 through 125' Processing helix chain 'Q' and resid 216 through 226 Processing helix chain 'Q' and resid 256 through 263 removed outlier: 4.210A pdb=" N ARG Q 261 " --> pdb=" O LEU Q 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 74 through 77 No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 84 through 86 No H-bonds generated for 'chain 'R' and resid 84 through 86' Processing helix chain 'R' and resid 96 through 104 removed outlier: 4.992A pdb=" N LEU R 104 " --> pdb=" O GLY R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 145 Processing helix chain 'R' and resid 153 through 167 removed outlier: 4.089A pdb=" N ARG R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 199 Processing helix chain 'R' and resid 212 through 217 removed outlier: 4.240A pdb=" N ARG R 216 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 260 removed outlier: 4.405A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 127 through 129 No H-bonds generated for 'chain 'S' and resid 127 through 129' Processing helix chain 'S' and resid 164 through 172 Processing helix chain 'T' and resid 15 through 33 Proline residue: T 21 - end of helix removed outlier: 3.533A pdb=" N ASP T 25 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE T 28 " --> pdb=" O ASP T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 67 removed outlier: 3.690A pdb=" N ILE T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 84 Processing helix chain 'T' and resid 89 through 96 Processing helix chain 'T' and resid 99 through 102 removed outlier: 4.490A pdb=" N LYS T 102 " --> pdb=" O GLY T 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 99 through 102' Processing helix chain 'T' and resid 126 through 135 removed outlier: 4.242A pdb=" N GLU T 131 " --> pdb=" O ALA T 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 22 Processing helix chain 'Z' and resid 26 through 30 Processing helix chain 'Z' and resid 37 through 45 Processing helix chain 'Z' and resid 50 through 65 removed outlier: 3.949A pdb=" N ARG Z 53 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN Z 54 " --> pdb=" O ILE Z 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE Z 63 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR Z 64 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU Z 65 " --> pdb=" O ASP Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 84 removed outlier: 3.983A pdb=" N SER Z 77 " --> pdb=" O ILE Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 107 Processing helix chain 'Z' and resid 111 through 127 removed outlier: 3.753A pdb=" N TYR Z 127 " --> pdb=" O ILE Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 144 Processing helix chain 'Z' and resid 148 through 165 removed outlier: 5.704A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 183 removed outlier: 3.739A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 202 removed outlier: 3.945A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE Z 198 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 306 through 315 removed outlier: 3.927A pdb=" N HIS Z 310 " --> pdb=" O ASP Z 306 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 335 Processing helix chain 'Z' and resid 341 through 353 removed outlier: 4.117A pdb=" N PHE Z 353 " --> pdb=" O ARG Z 349 " (cutoff:3.500A) Processing helix chain 'Z' and resid 355 through 370 Processing helix chain 'Z' and resid 372 through 375 Processing helix chain 'Z' and resid 380 through 393 removed outlier: 4.542A pdb=" N GLY Z 385 " --> pdb=" O ARG Z 382 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS Z 386 " --> pdb=" O ILE Z 383 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP Z 388 " --> pdb=" O GLY Z 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS Z 390 " --> pdb=" O PHE Z 387 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER Z 393 " --> pdb=" O HIS Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 399 through 404 removed outlier: 3.751A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 431 removed outlier: 4.254A pdb=" N ASN Z 429 " --> pdb=" O GLN Z 425 " (cutoff:3.500A) Processing helix chain 'Z' and resid 435 through 441 Processing helix chain 'Z' and resid 455 through 467 Processing helix chain 'Z' and resid 475 through 484 Processing helix chain 'c' and resid 15 through 28 Processing helix chain 'c' and resid 30 through 39 removed outlier: 3.530A pdb=" N TRP c 33 " --> pdb=" O THR c 30 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER c 34 " --> pdb=" O HIS c 31 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA c 37 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU c 39 " --> pdb=" O VAL c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 67 through 79 Processing helix chain 'c' and resid 84 through 91 Processing helix chain 'c' and resid 95 through 107 Processing helix chain 'c' and resid 147 through 158 Processing helix chain 'c' and resid 165 through 193 Processing helix chain 'c' and resid 233 through 251 removed outlier: 4.261A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 338 through 355 removed outlier: 3.785A pdb=" N UNK c 355 " --> pdb=" O UNK c 351 " (cutoff:3.500A) Processing helix chain 'c' and resid 359 through 363 Processing helix chain 'c' and resid 374 through 381 Processing helix chain 'c' and resid 385 through 400 removed outlier: 3.637A pdb=" N UNK c 390 " --> pdb=" O UNK c 386 " (cutoff:3.500A) Processing helix chain 'c' and resid 423 through 437 removed outlier: 3.595A pdb=" N UNK c 427 " --> pdb=" O UNK c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 468 removed outlier: 3.505A pdb=" N UNK c 450 " --> pdb=" O UNK c 446 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N UNK c 468 " --> pdb=" O UNK c 464 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 586 removed outlier: 3.597A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) Proline residue: c 504 - end of helix removed outlier: 4.515A pdb=" N SER c 515 " --> pdb=" O GLU c 511 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS c 516 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS c 526 " --> pdb=" O GLN c 522 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.688A pdb=" N GLN c 536 " --> pdb=" O PRO c 532 " (cutoff:3.500A) Proline residue: c 550 - end of helix removed outlier: 3.965A pdb=" N ILE c 553 " --> pdb=" O LEU c 549 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU c 554 " --> pdb=" O PRO c 550 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN c 556 " --> pdb=" O LEU c 552 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER c 572 " --> pdb=" O GLN c 568 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 577 " --> pdb=" O LEU c 573 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS c 578 " --> pdb=" O GLU c 574 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG c 579 " --> pdb=" O GLY c 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU c 580 " --> pdb=" O ARG c 576 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU c 584 " --> pdb=" O LEU c 580 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN c 585 " --> pdb=" O GLN c 581 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER c 586 " --> pdb=" O ALA c 582 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 60 removed outlier: 3.609A pdb=" N LYS d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 77 Processing helix chain 'd' and resid 81 through 94 Processing helix chain 'd' and resid 99 through 110 removed outlier: 4.041A pdb=" N GLU d 109 " --> pdb=" O TYR d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 128 removed outlier: 4.073A pdb=" N MET d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 145 Processing helix chain 'd' and resid 149 through 161 Processing helix chain 'd' and resid 166 through 178 removed outlier: 4.184A pdb=" N ARG d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.909A pdb=" N ARG d 186 " --> pdb=" O TRP d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 212 Processing helix chain 'd' and resid 215 through 235 removed outlier: 3.811A pdb=" N THR d 228 " --> pdb=" O LEU d 224 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN d 234 " --> pdb=" O ALA d 230 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU d 235 " --> pdb=" O ASN d 231 " (cutoff:3.500A) Processing helix chain 'd' and resid 240 through 257 Processing helix chain 'd' and resid 260 through 273 Processing helix chain 'd' and resid 298 through 310 Processing helix chain 'd' and resid 317 through 332 Processing helix chain 'd' and resid 341 through 353 Processing helix chain 'd' and resid 361 through 368 removed outlier: 3.812A pdb=" N UNK d 366 " --> pdb=" O UNK d 362 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK d 367 " --> pdb=" O UNK d 363 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNK d 368 " --> pdb=" O UNK d 364 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 374 Processing helix chain 'd' and resid 380 through 389 Processing helix chain 'd' and resid 394 through 400 Processing helix chain 'd' and resid 413 through 423 removed outlier: 3.950A pdb=" N UNK d 418 " --> pdb=" O UNK d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 443 removed outlier: 3.501A pdb=" N UNK d 443 " --> pdb=" O UNK d 439 " (cutoff:3.500A) Processing helix chain 'd' and resid 454 through 462 Processing helix chain 'd' and resid 469 through 479 removed outlier: 3.676A pdb=" N UNK d 473 " --> pdb=" O UNK d 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK d 479 " --> pdb=" O UNK d 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 488 through 498 removed outlier: 3.670A pdb=" N UNK d 494 " --> pdb=" O UNK d 490 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK d 498 " --> pdb=" O UNK d 494 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 515 Processing helix chain 'd' and resid 520 through 527 Processing helix chain 'd' and resid 539 through 550 Processing helix chain 'd' and resid 561 through 575 removed outlier: 3.692A pdb=" N UNK d 575 " --> pdb=" O UNK d 571 " (cutoff:3.500A) Processing helix chain 'd' and resid 585 through 594 Processing helix chain 'd' and resid 602 through 619 Processing helix chain 'I' and resid 97 through 121 removed outlier: 3.751A pdb=" N ALA I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 189 Processing helix chain 'I' and resid 198 through 210 Processing helix chain 'v' and resid 157 through 168 Processing helix chain 'v' and resid 172 through 182 Processing helix chain 'v' and resid 187 through 200 Processing helix chain 'v' and resid 205 through 217 Processing helix chain 'v' and resid 221 through 232 Processing helix chain 'v' and resid 237 through 249 Processing helix chain 'v' and resid 255 through 266 Processing helix chain 'v' and resid 270 through 282 removed outlier: 3.608A pdb=" N UNK v 276 " --> pdb=" O UNK v 272 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 298 Processing helix chain 'v' and resid 302 through 314 Processing helix chain 'v' and resid 320 through 333 Processing helix chain 'v' and resid 338 through 350 Processing helix chain 'v' and resid 356 through 365 removed outlier: 3.585A pdb=" N UNK v 363 " --> pdb=" O UNK v 360 " (cutoff:3.500A) Processing helix chain 'v' and resid 369 through 381 Processing helix chain 'v' and resid 388 through 400 Processing helix chain 'v' and resid 404 through 414 Processing helix chain 'v' and resid 421 through 436 Processing helix chain 'v' and resid 441 through 458 removed outlier: 4.253A pdb=" N UNK v 457 " --> pdb=" O UNK v 453 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK v 458 " --> pdb=" O UNK v 454 " (cutoff:3.500A) Processing helix chain 'v' and resid 464 through 482 Processing helix chain 'v' and resid 488 through 500 Processing helix chain 'v' and resid 505 through 523 Processing helix chain 'v' and resid 528 through 541 removed outlier: 3.537A pdb=" N UNK v 534 " --> pdb=" O UNK v 530 " (cutoff:3.500A) Processing helix chain 'v' and resid 547 through 559 removed outlier: 4.178A pdb=" N UNK v 556 " --> pdb=" O UNK v 553 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N UNK v 557 " --> pdb=" O UNK v 554 " (cutoff:3.500A) Processing helix chain 'v' and resid 570 through 578 removed outlier: 4.380A pdb=" N VAL v 577 " --> pdb=" O ALA v 573 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE v 578 " --> pdb=" O TYR v 574 " (cutoff:3.500A) Processing helix chain 'v' and resid 585 through 597 Processing helix chain 'v' and resid 602 through 635 Proline residue: v 613 - end of helix Proline residue: v 616 - end of helix removed outlier: 4.277A pdb=" N ILE v 619 " --> pdb=" O PHE v 615 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR v 621 " --> pdb=" O PRO v 617 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU v 622 " --> pdb=" O GLU v 618 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU v 626 " --> pdb=" O GLU v 622 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN v 635 " --> pdb=" O ALA v 631 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 652 Processing helix chain 'v' and resid 664 through 675 removed outlier: 4.047A pdb=" N ARG v 675 " --> pdb=" O VAL v 671 " (cutoff:3.500A) Processing helix chain 'v' and resid 680 through 688 Processing helix chain 'v' and resid 707 through 719 Processing helix chain 'v' and resid 723 through 733 removed outlier: 3.722A pdb=" N GLU v 727 " --> pdb=" O SER v 723 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN v 730 " --> pdb=" O ARG v 726 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU v 731 " --> pdb=" O GLU v 727 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 755 removed outlier: 4.292A pdb=" N UNK v 751 " --> pdb=" O UNK v 747 " (cutoff:3.500A) Processing helix chain 'v' and resid 760 through 772 Processing helix chain 'v' and resid 780 through 791 Processing helix chain 'v' and resid 798 through 817 Processing helix chain 'n' and resid 53 through 62 removed outlier: 4.060A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR n 62 " --> pdb=" O ARG n 58 " (cutoff:3.500A) Processing helix chain 'n' and resid 424 through 426 No H-bonds generated for 'chain 'n' and resid 424 through 426' Processing helix chain 'o' and resid 25 through 34 removed outlier: 3.725A pdb=" N GLN o 30 " --> pdb=" O SER o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 139 removed outlier: 3.723A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE o 96 " --> pdb=" O MET o 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU o 98 " --> pdb=" O GLU o 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR o 101 " --> pdb=" O LYS o 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER o 104 " --> pdb=" O SER o 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS o 107 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL o 122 " --> pdb=" O ALA o 118 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) Proline residue: o 138 - end of helix Processing helix chain 'p' and resid 25 through 34 removed outlier: 3.590A pdb=" N LYS p 33 " --> pdb=" O GLU p 29 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 141 removed outlier: 3.594A pdb=" N GLU p 94 " --> pdb=" O ALA p 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET p 128 " --> pdb=" O ALA p 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU p 132 " --> pdb=" O MET p 128 " (cutoff:3.500A) Proline residue: p 138 - end of helix removed outlier: 3.648A pdb=" N SER p 141 " --> pdb=" O LEU p 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 34 Processing helix chain 'q' and resid 78 through 142 removed outlier: 3.656A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS q 108 " --> pdb=" O SER q 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS q 135 " --> pdb=" O ASN q 131 " (cutoff:3.500A) Proline residue: q 138 - end of helix Processing helix chain 'q' and resid 473 through 475 No H-bonds generated for 'chain 'q' and resid 473 through 475' Processing helix chain 'r' and resid 25 through 34 Processing helix chain 'r' and resid 78 through 138 removed outlier: 3.717A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU r 93 " --> pdb=" O ASP r 89 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG r 99 " --> pdb=" O ASN r 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR r 101 " --> pdb=" O LYS r 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU r 115 " --> pdb=" O THR r 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS r 120 " --> pdb=" O ARG r 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Proline residue: r 138 - end of helix Processing helix chain 't' and resid 14 through 31 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 83 through 102 removed outlier: 3.579A pdb=" N LYS t 94 " --> pdb=" O GLU t 90 " (cutoff:3.500A) Proline residue: t 96 - end of helix Processing helix chain 't' and resid 104 through 109 removed outlier: 4.054A pdb=" N SER t 109 " --> pdb=" O PRO t 105 " (cutoff:3.500A) Processing helix chain 't' and resid 112 through 174 removed outlier: 3.654A pdb=" N VAL t 117 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR t 120 " --> pdb=" O ILE t 116 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL t 127 " --> pdb=" O HIS t 123 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP t 129 " --> pdb=" O GLU t 125 " (cutoff:3.500A) Proline residue: t 133 - end of helix removed outlier: 3.741A pdb=" N ARG t 148 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU t 155 " --> pdb=" O CYS t 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG t 172 " --> pdb=" O LEU t 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 15 No H-bonds generated for 'chain 'k' 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 'h' and resid 15 through 21 Processing helix chain 'h' and resid 75 through 77 No H-bonds generated for 'chain 'h' 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 'g' and resid 16 through 28 Processing helix chain 'g' and resid 32 through 40 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'G' and resid 13 through 23 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'H' and resid 15 through 21 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'U' and resid 6 through 14 Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 103 through 107 Processing helix chain 'X' and resid 41 through 55 removed outlier: 4.195A pdb=" N THR X 54 " --> pdb=" O LEU X 50 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE X 55 " --> pdb=" O LEU X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 88 Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.511A pdb=" N ASP Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 50 Processing helix chain 'Y' and resid 111 through 119 removed outlier: 4.608A pdb=" N ARG Y 116 " --> pdb=" O ASP Y 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG Y 119 " --> pdb=" O ARG Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 136 Processing helix chain 'Y' and resid 140 through 147 Processing helix chain 'e' and resid 311 through 313 No H-bonds generated for 'chain 'e' and resid 311 through 313' Processing helix chain 'e' and resid 323 through 331 Processing helix chain 'e' and resid 338 through 349 Processing helix chain 'e' and resid 351 through 365 removed outlier: 6.210A pdb=" N SER e 357 " --> pdb=" O ARG e 354 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU e 359 " --> pdb=" O ARG e 356 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE e 363 " --> pdb=" O LEU e 360 " (cutoff:3.500A) Processing helix chain 'e' and resid 379 through 386 removed outlier: 3.779A pdb=" N ALA e 384 " --> pdb=" O THR e 380 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN e 385 " --> pdb=" O THR e 381 " (cutoff:3.500A) Processing helix chain 'e' and resid 393 through 396 Processing helix chain 'e' and resid 407 through 421 Processing helix chain 'e' and resid 451 through 460 Processing helix chain 'e' and resid 480 through 495 removed outlier: 3.676A pdb=" N ALA e 494 " --> pdb=" O LYS e 490 " (cutoff:3.500A) Processing helix chain 'e' and resid 511 through 516 Processing helix chain 'e' and resid 544 through 557 Processing helix chain 'e' and resid 559 through 561 No H-bonds generated for 'chain 'e' and resid 559 through 561' Processing helix chain 'e' and resid 573 through 593 removed outlier: 3.666A pdb=" N SER e 592 " --> pdb=" O LEU e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 617 through 624 removed outlier: 3.576A pdb=" N ILE e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE e 624 " --> pdb=" O GLN e 620 " (cutoff:3.500A) Processing helix chain 'e' and resid 639 through 643 removed outlier: 3.849A pdb=" N THR e 643 " --> pdb=" O ILE e 640 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 691 removed outlier: 4.021A pdb=" N ALA e 690 " --> pdb=" O ARG e 686 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY e 691 " --> pdb=" O SER e 687 " (cutoff:3.500A) Processing helix chain 'e' and resid 704 through 708 Processing helix chain 'e' and resid 725 through 733 Processing helix chain 'e' and resid 751 through 764 Processing helix chain 'e' and resid 775 through 782 Processing helix chain 'e' and resid 787 through 795 Processing helix chain 'e' and resid 802 through 810 Processing helix chain 'e' and resid 825 through 835 removed outlier: 3.823A pdb=" N PHE e 835 " --> pdb=" O ALA e 831 " (cutoff:3.500A) Processing helix chain 'e' and resid 841 through 852 Processing helix chain 'e' and resid 858 through 865 Processing helix chain 'e' and resid 869 through 888 Processing helix chain 'e' and resid 899 through 911 Processing helix chain 'e' and resid 972 through 979 Processing helix chain 'f' and resid 81 through 87 removed outlier: 3.927A pdb=" N ILE f 85 " --> pdb=" O GLN f 82 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA f 86 " --> pdb=" O GLU f 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 99 No H-bonds generated for 'chain 'f' and resid 97 through 99' Processing helix chain 'f' and resid 106 through 130 removed outlier: 5.390A pdb=" N GLU f 129 " --> pdb=" O LYS f 125 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA f 130 " --> pdb=" O ALA f 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 133 through 152 removed outlier: 4.703A pdb=" N LEU f 137 " --> pdb=" O PRO f 133 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP f 138 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 145 - end of helix Processing helix chain 'f' and resid 157 through 171 Processing helix chain 'f' and resid 173 through 188 removed outlier: 3.584A pdb=" N ILE f 176 " --> pdb=" O PRO f 173 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN f 177 " --> pdb=" O LYS f 174 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN f 181 " --> pdb=" O LEU f 178 " (cutoff:3.500A) Processing helix chain 'f' and resid 224 through 245 removed outlier: 3.555A pdb=" N SER f 232 " --> pdb=" O LEU f 228 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS f 234 " --> pdb=" O ILE f 230 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG f 235 " --> pdb=" O THR f 231 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 968 through 973 Processing sheet with id= D, first strand: chain 'A' and resid 1247 through 1251 removed outlier: 3.804A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= F, first strand: chain 'A' and resid 1258 through 1262 removed outlier: 6.896A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) 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 1738 removed outlier: 6.326A pdb=" N VAL A1773 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN A1737 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A1775 " --> pdb=" O GLN A1737 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1932 through 1934 removed outlier: 3.886A pdb=" N LEU A1850 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 7.534A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 320 through 322 removed outlier: 9.426A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.298A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.580A pdb=" N LYS C 474 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= P, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= Q, first strand: chain 'C' and resid 710 through 714 removed outlier: 6.794A pdb=" N VAL C 773 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU C 820 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 775 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 767 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 927 through 929 removed outlier: 6.976A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 219 through 221 removed outlier: 4.246A pdb=" N THR O 205 " --> pdb=" O SER O 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER O 201 " --> pdb=" O THR O 205 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER O 199 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 229 through 233 removed outlier: 4.520A pdb=" N LEU O 238 " --> pdb=" O HIS O 233 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY O 243 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL O 247 " --> pdb=" O GLY O 243 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 269 through 274 removed outlier: 6.799A pdb=" N SER O 284 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL O 272 " --> pdb=" O VAL O 282 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL O 282 " --> pdb=" O VAL O 272 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR O 289 " --> pdb=" O SER O 285 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 314 through 316 Processing sheet with id= W, first strand: chain 'O' and resid 385 through 388 removed outlier: 3.870A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR O 355 " --> pdb=" O GLY O 367 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 404 through 407 removed outlier: 4.314A pdb=" N CYS O 404 " --> pdb=" O GLY O 417 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY O 417 " --> pdb=" O CYS O 404 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 164 through 167 Processing sheet with id= Z, first strand: chain 'Q' and resid 241 through 243 Processing sheet with id= AA, first strand: chain 'R' and resid 222 through 225 removed outlier: 3.853A pdb=" N CYS R 181 " --> pdb=" O VAL R 176 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= AC, first strand: chain 'n' and resid 168 through 170 Processing sheet with id= AD, first strand: chain 'n' and resid 211 through 214 Processing sheet with id= AE, first strand: chain 'n' and resid 287 through 289 removed outlier: 3.532A pdb=" N ILE n 272 " --> pdb=" O TYR n 289 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'n' and resid 296 through 301 removed outlier: 6.922A pdb=" N SER n 311 " --> pdb=" O LEU n 297 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU n 299 " --> pdb=" O ILE n 309 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE n 309 " --> pdb=" O LEU n 299 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE n 308 " --> pdb=" O TRP n 320 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'n' and resid 342 through 344 Processing sheet with id= AH, first strand: chain 'n' and resid 381 through 383 removed outlier: 3.749A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP n 402 " --> pdb=" O PHE n 408 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE n 408 " --> pdb=" O ASP n 402 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'n' and resid 442 through 446 removed outlier: 3.866A pdb=" N LYS n 450 " --> pdb=" O GLY n 446 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP n 455 " --> pdb=" O VAL n 154 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL n 154 " --> pdb=" O ASP n 455 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'n' and resid 187 through 190 removed outlier: 3.586A pdb=" N ARG n 200 " --> pdb=" O ILE n 189 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'o' and resid 13 through 15 Processing sheet with id= AL, first strand: chain 'p' and resid 13 through 15 Processing sheet with id= AM, first strand: chain 'q' and resid 13 through 15 Processing sheet with id= AN, first strand: chain 'q' and resid 162 through 164 removed outlier: 3.609A pdb=" N GLN q 468 " --> pdb=" O CYS q 481 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'q' and resid 175 through 180 removed outlier: 6.254A pdb=" N TYR q 197 " --> pdb=" O ILE q 176 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS q 178 " --> pdb=" O PHE q 195 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE q 195 " --> pdb=" O LYS q 178 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG q 214 " --> pdb=" O LEU q 220 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU q 220 " --> pdb=" O ARG q 214 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'q' and resid 232 through 235 removed outlier: 5.636A pdb=" N ASN q 274 " --> pdb=" O PRO q 262 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'q' and resid 292 through 295 removed outlier: 3.594A pdb=" N TYR q 292 " --> pdb=" O ALA q 305 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'q' and resid 333 through 338 removed outlier: 6.250A pdb=" N TYR q 348 " --> pdb=" O SER q 334 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY q 336 " --> pdb=" O ALA q 346 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA q 346 " --> pdb=" O GLY q 336 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU q 338 " --> pdb=" O LEU q 344 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU q 344 " --> pdb=" O LEU q 338 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN q 358 " --> pdb=" O GLN q 364 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN q 364 " --> pdb=" O ASN q 358 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'q' and resid 379 through 382 removed outlier: 3.759A pdb=" N LEU q 409 " --> pdb=" O CYS q 399 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP q 401 " --> pdb=" O GLY q 407 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY q 407 " --> pdb=" O ASP q 401 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'q' and resid 457 through 459 Processing sheet with id= AU, first strand: chain 'r' and resid 13 through 16 removed outlier: 4.188A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'k' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'k' and resid 43 through 45 Processing sheet with id= AX, first strand: chain 'i' and resid 58 through 61 removed outlier: 3.543A pdb=" N GLN i 34 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU i 31 " --> pdb=" O GLN i 34 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY i 36 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N ILE i 29 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N ARG i 38 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL i 27 " --> pdb=" O ARG i 38 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'i' and resid 52 through 54 removed outlier: 3.847A 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= AZ, first strand: chain 'h' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU h 58 " --> pdb=" O THR h 67 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR h 67 " --> pdb=" O GLU h 58 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 71 through 73 removed outlier: 3.636A pdb=" N GLN h 52 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER h 44 " --> pdb=" O GLN h 52 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN h 54 " --> pdb=" O LEU h 42 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU h 42 " --> pdb=" O ASN h 54 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 28 through 31 removed outlier: 4.002A pdb=" N TYR h 80 " --> pdb=" O LYS h 30 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'j' and resid 23 through 25 Processing sheet with id= BD, first strand: chain 'j' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP j 41 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU j 29 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'l' and resid 69 through 73 removed outlier: 6.948A pdb=" N GLU l 22 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER l 20 " --> pdb=" O ILE l 72 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN l 43 " --> pdb=" O VAL l 34 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'l' and resid 47 through 50 Processing sheet with id= BG, 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= BH, 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= BI, first strand: chain 'g' and resid 87 through 91 removed outlier: 3.576A pdb=" N ARG g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'g' and resid 67 through 70 Processing sheet with id= BK, first strand: chain 'F' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS F 48 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'F' and resid 43 through 45 Processing sheet with id= BM, first strand: chain 'G' and resid 58 through 61 removed outlier: 3.544A pdb=" N GLN G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU G 31 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLY G 36 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE G 29 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ARG G 38 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N VAL G 27 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'G' and resid 52 through 54 removed outlier: 3.846A pdb=" N VAL G 52 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 82 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU H 58 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR H 67 " --> pdb=" O GLU H 58 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 71 through 73 removed outlier: 3.637A pdb=" N GLN H 52 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER H 44 " --> pdb=" O GLN H 52 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN H 54 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU H 42 " --> pdb=" O ASN H 54 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 28 through 31 removed outlier: 4.003A pdb=" N TYR H 80 " --> pdb=" O LYS H 30 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'K' and resid 23 through 25 Processing sheet with id= BS, 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= BT, first strand: chain 'U' and resid 69 through 73 removed outlier: 6.949A pdb=" N GLU U 22 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE U 72 " --> pdb=" O SER U 20 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER U 20 " --> pdb=" O ILE U 72 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN U 43 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'U' and resid 47 through 50 Processing sheet with id= BV, first strand: chain 'V' and resid 80 through 82 removed outlier: 3.706A pdb=" N GLU V 13 " --> pdb=" O LEU V 29 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'V' and resid 84 through 87 removed outlier: 6.501A pdb=" N THR V 41 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU V 29 " --> pdb=" O THR V 41 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'W' and resid 53 through 55 removed outlier: 3.577A pdb=" N ARG W 89 " --> pdb=" O GLU W 74 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'W' and resid 67 through 70 Processing sheet with id= BZ, first strand: chain 'W' and resid 45 through 48 removed outlier: 3.636A pdb=" N VAL W 103 " --> pdb=" O SER W 47 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'X' and resid 72 through 74 Processing sheet with id= CB, first strand: chain 'Y' and resid 13 through 15 removed outlier: 7.107A pdb=" N ILE Y 56 " --> pdb=" O LEU Y 36 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR Y 78 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN Y 100 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN Y 126 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 522 through 524 removed outlier: 8.917A pdb=" N PHE e 523 " --> pdb=" O VAL e 368 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL e 370 " --> pdb=" O PHE e 523 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU e 501 " --> pdb=" O VAL e 369 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE e 371 " --> pdb=" O LEU e 501 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE e 503 " --> pdb=" O ILE e 371 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER e 399 " --> pdb=" O SER e 468 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL e 470 " --> pdb=" O SER e 399 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL e 401 " --> pdb=" O VAL e 470 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE e 472 " --> pdb=" O VAL e 401 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR e 403 " --> pdb=" O ILE e 472 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 606 through 611 removed outlier: 6.827A pdb=" N ARG e 632 " --> pdb=" O GLU e 607 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU e 609 " --> pdb=" O ARG e 632 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE e 634 " --> pdb=" O LEU e 609 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE e 611 " --> pdb=" O ILE e 634 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE e 636 " --> pdb=" O ILE e 611 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE e 566 " --> pdb=" O ILE e 635 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA e 637 " --> pdb=" O ILE e 566 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE e 568 " --> pdb=" O ALA e 637 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU e 567 " --> pdb=" O ARG e 651 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL e 653 " --> pdb=" O LEU e 567 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE e 569 " --> pdb=" O VAL e 653 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP e 655 " --> pdb=" O PHE e 569 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR e 697 " --> pdb=" O VAL e 653 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASP e 655 " --> pdb=" O THR e 697 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR e 699 " --> pdb=" O ASP e 655 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 658 through 665 Processing sheet with id= CF, first strand: chain 'e' and resid 950 through 952 Processing sheet with id= CG, first strand: chain 'e' and resid 955 through 958 3157 hydrogen bonds defined for protein. 8646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 213 hydrogen bonds 386 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 156 stacking parallelities Total time for adding SS restraints: 46.11 Time building geometry restraints manager: 28.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.56: 77409 1.56 - 1.92: 1189 1.92 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 78599 Sorted by residual: bond pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 1.335 2.990 -1.655 1.97e-02 2.58e+03 7.06e+03 bond pdb=" CB CYS n 399 " pdb=" SG CYS n 399 " ideal model delta sigma weight residual 1.808 1.408 0.400 3.30e-02 9.18e+02 1.47e+02 bond pdb=" CB CYS n 444 " pdb=" SG CYS n 444 " ideal model delta sigma weight residual 1.808 1.429 0.379 3.30e-02 9.18e+02 1.32e+02 bond pdb=" CA ASP Y 69 " pdb=" CB ASP Y 69 " ideal model delta sigma weight residual 1.532 1.381 0.151 1.42e-02 4.96e+03 1.13e+02 bond pdb=" CB CYS n 454 " pdb=" SG CYS n 454 " ideal model delta sigma weight residual 1.808 1.479 0.329 3.30e-02 9.18e+02 9.92e+01 ... (remaining 78594 not shown) Histogram of bond angle deviations from ideal: 84.57 - 95.86: 8 95.86 - 107.15: 5009 107.15 - 118.44: 60111 118.44 - 129.73: 42348 129.73 - 141.02: 646 Bond angle restraints: 108122 Sorted by residual: angle pdb=" O ALA q 247 " pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 122.59 84.57 38.02 1.33e+00 5.65e-01 8.17e+02 angle pdb=" N PRO Y 44 " pdb=" CA PRO Y 44 " pdb=" CB PRO Y 44 " ideal model delta sigma weight residual 103.23 113.92 -10.69 6.70e-01 2.23e+00 2.55e+02 angle pdb=" C ALA q 247 " pdb=" N ARG q 256 " pdb=" CA ARG q 256 " ideal model delta sigma weight residual 120.17 141.02 -20.85 1.54e+00 4.22e-01 1.83e+02 angle pdb=" C LEU Y 81 " pdb=" N GLY Y 82 " pdb=" CA GLY Y 82 " ideal model delta sigma weight residual 120.10 131.58 -11.48 9.50e-01 1.11e+00 1.46e+02 angle pdb=" N PHE e 595 " pdb=" CA PHE e 595 " pdb=" C PHE e 595 " ideal model delta sigma weight residual 108.60 123.45 -14.85 1.46e+00 4.69e-01 1.03e+02 ... (remaining 108117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 46772 35.94 - 71.88: 1333 71.88 - 107.83: 132 107.83 - 143.77: 34 143.77 - 179.71: 21 Dihedral angle restraints: 48292 sinusoidal: 20589 harmonic: 27703 Sorted by residual: dihedral pdb=" CA GLY n 67 " pdb=" C GLY n 67 " pdb=" N PRO n 68 " pdb=" CA PRO n 68 " ideal model delta harmonic sigma weight residual -180.00 -51.01 -128.99 0 5.00e+00 4.00e-02 6.66e+02 dihedral pdb=" CA ALA l 81 " pdb=" C ALA l 81 " pdb=" N PRO l 82 " pdb=" CA PRO l 82 " ideal model delta harmonic sigma weight residual -180.00 -52.74 -127.26 0 5.00e+00 4.00e-02 6.48e+02 dihedral pdb=" CA ALA U 81 " pdb=" C ALA U 81 " pdb=" N PRO U 82 " pdb=" CA PRO U 82 " ideal model delta harmonic sigma weight residual -180.00 -52.83 -127.17 0 5.00e+00 4.00e-02 6.47e+02 ... (remaining 48289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 12803 0.243 - 0.485: 145 0.485 - 0.728: 14 0.728 - 0.971: 5 0.971 - 1.214: 1 Chirality restraints: 12968 Sorted by residual: chirality pdb=" CA LYS e 631 " pdb=" N LYS e 631 " pdb=" C LYS e 631 " pdb=" CB LYS e 631 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA PHE e 595 " pdb=" N PHE e 595 " pdb=" C PHE e 595 " pdb=" CB PHE e 595 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA ASN e 923 " pdb=" N ASN e 923 " pdb=" C ASN e 923 " pdb=" CB ASN e 923 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 12965 not shown) Planarity restraints: 12497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA q 247 " 0.167 2.00e-02 2.50e+03 2.29e-01 5.23e+02 pdb=" C ALA q 247 " -0.387 2.00e-02 2.50e+03 pdb=" O ALA q 247 " 0.171 2.00e-02 2.50e+03 pdb=" N ARG q 256 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 81 " -0.033 2.00e-02 2.50e+03 6.89e-02 4.74e+01 pdb=" C ALA U 81 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA U 81 " -0.045 2.00e-02 2.50e+03 pdb=" N PRO U 82 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA l 81 " 0.033 2.00e-02 2.50e+03 6.84e-02 4.68e+01 pdb=" C ALA l 81 " -0.118 2.00e-02 2.50e+03 pdb=" O ALA l 81 " 0.045 2.00e-02 2.50e+03 pdb=" N PRO l 82 " 0.040 2.00e-02 2.50e+03 ... (remaining 12494 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 253 2.24 - 2.91: 35596 2.91 - 3.57: 112064 3.57 - 4.24: 176260 4.24 - 4.90: 281203 Nonbonded interactions: 605376 Sorted by model distance: nonbonded pdb=" NZ LYS C 99 " pdb=" OP2 G D 43 " model vdw 1.580 2.520 nonbonded pdb=" P G N 100 " pdb=" O2' A M 501 " model vdw 1.599 3.400 nonbonded pdb=" OP2 U E 21 " pdb=" OG SER n 54 " model vdw 1.708 2.440 nonbonded pdb=" CB GLN c 193 " pdb=" CG PRO n 436 " model vdw 1.726 3.840 nonbonded pdb=" CE2 PHE R 75 " pdb=" C8 A E 35 " model vdw 1.741 3.560 ... (remaining 605371 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 'F' selection = (chain 'k' 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)) } ncs_group { reference = chain 'G' selection = chain 'i' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'K' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'l' } ncs_group { reference = chain 'V' selection = chain 'm' } ncs_group { reference = (chain 'o' and (resid 1 through 52 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 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'p' and (resid 1 through 52 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 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'r' and (resid 1 through 52 or resid 57 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.930 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 203.580 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 229.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 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 : 0.015 1.655 78599 Z= 0.986 Angle : 1.474 38.022 108122 Z= 0.872 Chirality : 0.083 1.214 12968 Planarity : 0.008 0.229 12497 Dihedral : 16.802 179.710 30142 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 1.58 % Allowed : 12.54 % Favored : 85.88 % Rotamer: Outliers : 1.96 % Allowed : 3.85 % Favored : 94.19 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.04 % Twisted Proline : 3.29 % Twisted General : 1.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.07), residues: 8398 helix: -3.46 (0.06), residues: 3400 sheet: -2.42 (0.13), residues: 1164 loop : -3.20 (0.08), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP A 823 HIS 0.028 0.004 HIS A 675 PHE 0.050 0.004 PHE A1495 TYR 0.075 0.005 TYR f 168 ARG 0.034 0.002 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 7793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1301 time to evaluate : 5.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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