Starting phenix.real_space_refine on Fri Dec 8 09:47:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0w_12681/12_2023/7o0w_12681_updated.pdb" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 Fe 5 7.16 5 P 33 5.49 5 Mg 108 5.21 5 S 277 5.16 5 C 38980 2.51 5 N 7408 2.21 5 O 9665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BD PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 GLU 34": "OE1" <-> "OE2" Residue "ao TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bf TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56476 Number of models: 1 Model: "" Number of chains: 236 Chain: "AA" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BC" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BD" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BE" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BF" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BG" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BH" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BI" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BJ" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BK" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BL" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BM" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BN" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BO" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BP" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BQ" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BR" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BS" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BT" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BU" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BV" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BW" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BX" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2325 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 23, 'TRANS': 275} Chain: "C1" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 10, 'TRANS': 92} Chain: "C2" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "H1" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H2" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1404 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 163} Chain: "L" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2165 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2702 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain: "aa" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "ab" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ac" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ad" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ae" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "af" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ag" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ah" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ai" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aj" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ak" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "al" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "am" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "an" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ao" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ap" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ba" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bb" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bc" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bd" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "be" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bf" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bg" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bh" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bi" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bj" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bk" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bl" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bm" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bn" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "bo" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bp" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "CG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "MG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AB" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AD" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AE" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 303 Unusual residues: {'BCL': 3, 'LMT': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AF" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 268 Unusual residues: {'BCL': 3, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AK" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AM" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AN" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AO" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AP" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'0V9': 1, 'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AR" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AU" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AV" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'BCL': 2, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AX" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BA" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BB" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BC" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BD" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BE" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BF" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BH" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BI" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BJ" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BK" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BL" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BM" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BN" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BO" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BP" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BQ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BR" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BS" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BT" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BU" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BV" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BW" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BX" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 239 Unusual residues: {'HEC': 4, 'LMT': 1, 'NDG': 1, 'V75': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C1" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NDG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "H1" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 180 Unusual residues: {'0V9': 1, 'CD4': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 470 Unusual residues: {'0V9': 1, 'BCL': 2, 'BPH': 1, 'LMT': 5, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 526 Unusual residues: {' FE': 1, '0V9': 1, 'BCL': 2, 'BPH': 1, 'CD4': 2, 'CRT': 1, 'MQ8': 1, 'V75': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'0V9': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "ac" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ad" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 195 Unusual residues: {'0V9': 1, 'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "ae" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "af" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 292 Unusual residues: {'BCL': 1, 'CD4': 2, 'V7B': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ag" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'V7B': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ah" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ai" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'BCL': 1, 'UYH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "aj" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ak" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "al" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "am" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "an" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ao" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 119 Unusual residues: {'BCL': 1, 'MQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bb" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'0V9': 1, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bc" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "bd" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'0V9': 1, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "be" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bf" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bg" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bh" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bi" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bj" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bk" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bl" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bm" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bn" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bo" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bp" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AE" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AJ" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AK" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AL" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AN" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AR" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AS" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AV" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AW" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "C1" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "aa" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "ab" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "ad" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ae" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "af" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "ag" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "ah" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "ai" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "ak" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "al" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "am" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "an" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ao" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bb" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "be" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bf" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bg" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bh" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bk" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bl" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bm" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bn" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.09, per 1000 atoms: 0.39 Number of scatterers: 56476 At special positions: 0 Unit cell: (197.893, 196.894, 144.922, 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) Fe 5 26.01 S 277 16.00 P 33 15.00 Mg 108 11.99 O 9665 8.00 N 7408 7.00 C 38980 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=114, symmetry=0 Links applied BETA1-4 " MANCG 1 " - " RAMCG 2 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " MANMG 1 " - " RAMMG 2 " MAN-SER " MANMG 1 " - " SER M 331 " MAN-THR " MANCG 1 " - " THR C 108 " Number of additional bonds: simple=114, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.52 Conformation dependent library (CDL) restraints added in 5.3 seconds 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 4 sheets defined 66.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 5 No H-bonds generated for 'chain 'AA' and resid 3 through 5' Processing helix chain 'AA' and resid 10 through 35 Processing helix chain 'AA' and resid 40 through 46 Processing helix chain 'AB' and resid 3 through 5 No H-bonds generated for 'chain 'AB' and resid 3 through 5' Processing helix chain 'AB' and resid 10 through 36 Processing helix chain 'AB' and resid 40 through 46 Processing helix chain 'AC' and resid 3 through 5 No H-bonds generated for 'chain 'AC' and resid 3 through 5' Processing helix chain 'AC' and resid 10 through 35 Processing helix chain 'AC' and resid 40 through 45 Processing helix chain 'AD' and resid 3 through 5 No H-bonds generated for 'chain 'AD' and resid 3 through 5' Processing helix chain 'AD' and resid 10 through 36 Processing helix chain 'AD' and resid 40 through 46 Processing helix chain 'AE' and resid 3 through 7 removed outlier: 4.344A pdb=" N GLYAE 7 " --> pdb=" O ILEAE 4 " (cutoff:3.500A) Processing helix chain 'AE' and resid 10 through 35 Processing helix chain 'AE' and resid 40 through 46 removed outlier: 3.544A pdb=" N TYRAE 46 " --> pdb=" O LEUAE 42 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 5 No H-bonds generated for 'chain 'AF' and resid 3 through 5' Processing helix chain 'AF' and resid 10 through 35 Processing helix chain 'AF' and resid 40 through 46 Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 10 through 36 Processing helix chain 'AG' and resid 40 through 46 Processing helix chain 'AH' and resid 3 through 5 No H-bonds generated for 'chain 'AH' and resid 3 through 5' Processing helix chain 'AH' and resid 10 through 35 removed outlier: 3.528A pdb=" N GLYAH 34 " --> pdb=" O ILEAH 30 " (cutoff:3.500A) Processing helix chain 'AH' and resid 40 through 46 removed outlier: 3.523A pdb=" N TYRAH 46 " --> pdb=" O LEUAH 42 " (cutoff:3.500A) Processing helix chain 'AI' and resid 3 through 5 No H-bonds generated for 'chain 'AI' and resid 3 through 5' Processing helix chain 'AI' and resid 10 through 36 Processing helix chain 'AI' and resid 40 through 46 removed outlier: 3.661A pdb=" N TYRAI 46 " --> pdb=" O LEUAI 42 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 5 No H-bonds generated for 'chain 'AJ' and resid 3 through 5' Processing helix chain 'AJ' and resid 10 through 35 Processing helix chain 'AJ' and resid 40 through 45 Processing helix chain 'AK' and resid 3 through 5 No H-bonds generated for 'chain 'AK' and resid 3 through 5' Processing helix chain 'AK' and resid 10 through 35 removed outlier: 3.507A pdb=" N GLYAK 34 " --> pdb=" O ILEAK 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 40 through 46 Processing helix chain 'AL' and resid 3 through 5 No H-bonds generated for 'chain 'AL' and resid 3 through 5' Processing helix chain 'AL' and resid 10 through 36 Processing helix chain 'AL' and resid 40 through 46 Processing helix chain 'AM' and resid 3 through 5 No H-bonds generated for 'chain 'AM' and resid 3 through 5' Processing helix chain 'AM' and resid 10 through 36 Processing helix chain 'AM' and resid 40 through 46 Processing helix chain 'AN' and resid 3 through 5 No H-bonds generated for 'chain 'AN' and resid 3 through 5' Processing helix chain 'AN' and resid 10 through 36 Processing helix chain 'AN' and resid 40 through 45 Processing helix chain 'AO' and resid 3 through 5 No H-bonds generated for 'chain 'AO' and resid 3 through 5' Processing helix chain 'AO' and resid 10 through 36 Processing helix chain 'AO' and resid 40 through 46 Processing helix chain 'AP' and resid 3 through 5 No H-bonds generated for 'chain 'AP' and resid 3 through 5' Processing helix chain 'AP' and resid 10 through 36 Processing helix chain 'AP' and resid 40 through 46 Processing helix chain 'AQ' and resid 10 through 35 Processing helix chain 'AQ' and resid 40 through 46 removed outlier: 3.582A pdb=" N TYRAQ 46 " --> pdb=" O LEUAQ 42 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 5 No H-bonds generated for 'chain 'AR' and resid 3 through 5' Processing helix chain 'AR' and resid 10 through 36 Processing helix chain 'AR' and resid 40 through 46 removed outlier: 3.543A pdb=" N TYRAR 46 " --> pdb=" O LEUAR 42 " (cutoff:3.500A) Processing helix chain 'AS' and resid 3 through 5 No H-bonds generated for 'chain 'AS' and resid 3 through 5' Processing helix chain 'AS' and resid 10 through 35 Processing helix chain 'AS' and resid 40 through 46 removed outlier: 3.598A pdb=" N TYRAS 46 " --> pdb=" O LEUAS 42 " (cutoff:3.500A) Processing helix chain 'AT' and resid 3 through 5 No H-bonds generated for 'chain 'AT' and resid 3 through 5' Processing helix chain 'AT' and resid 10 through 35 Processing helix chain 'AT' and resid 40 through 46 Processing helix chain 'AU' and resid 3 through 5 No H-bonds generated for 'chain 'AU' and resid 3 through 5' Processing helix chain 'AU' and resid 10 through 36 Processing helix chain 'AU' and resid 40 through 46 Processing helix chain 'AV' and resid 3 through 5 No H-bonds generated for 'chain 'AV' and resid 3 through 5' Processing helix chain 'AV' and resid 10 through 36 Processing helix chain 'AV' and resid 40 through 46 Processing helix chain 'AW' and resid 3 through 5 No H-bonds generated for 'chain 'AW' and resid 3 through 5' Processing helix chain 'AW' and resid 10 through 35 removed outlier: 3.727A pdb=" N GLYAW 34 " --> pdb=" O ILEAW 30 " (cutoff:3.500A) Processing helix chain 'AW' and resid 40 through 46 removed outlier: 3.567A pdb=" N TYRAW 46 " --> pdb=" O LEUAW 42 " (cutoff:3.500A) Processing helix chain 'AX' and resid 10 through 36 Processing helix chain 'AX' and resid 40 through 46 removed outlier: 3.649A pdb=" N TYRAX 46 " --> pdb=" O LEUAX 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 9 through 40 removed outlier: 3.748A pdb=" N ARGBA 14 " --> pdb=" O GLUBA 10 " (cutoff:3.500A) Processing helix chain 'BB' and resid 9 through 40 removed outlier: 3.587A pdb=" N GLYBB 17 " --> pdb=" O ARGBB 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYRBB 18 " --> pdb=" O ARGBB 14 " (cutoff:3.500A) Processing helix chain 'BC' and resid 9 through 40 removed outlier: 3.680A pdb=" N TYRBC 18 " --> pdb=" O ARGBC 14 " (cutoff:3.500A) Processing helix chain 'BD' and resid 9 through 40 removed outlier: 3.665A pdb=" N GLYBD 17 " --> pdb=" O ARGBD 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYRBD 18 " --> pdb=" O ARGBD 14 " (cutoff:3.500A) Processing helix chain 'BE' and resid 9 through 40 removed outlier: 3.632A pdb=" N GLYBE 17 " --> pdb=" O ARGBE 13 " (cutoff:3.500A) Processing helix chain 'BF' and resid 9 through 40 Processing helix chain 'BG' and resid 9 through 40 removed outlier: 3.650A pdb=" N TYRBG 18 " --> pdb=" O ARGBG 14 " (cutoff:3.500A) Processing helix chain 'BH' and resid 9 through 40 Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 removed outlier: 3.648A pdb=" N TYRBJ 18 " --> pdb=" O ARGBJ 14 " (cutoff:3.500A) Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.678A pdb=" N GLYBK 17 " --> pdb=" O ARGBK 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 Processing helix chain 'BM' and resid 9 through 40 Processing helix chain 'BN' and resid 9 through 40 removed outlier: 3.580A pdb=" N TYRBN 18 " --> pdb=" O ARGBN 14 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.782A pdb=" N GLYBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYRBO 18 " --> pdb=" O ARGBO 14 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 removed outlier: 3.586A pdb=" N GLYBP 17 " --> pdb=" O ARGBP 13 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYRBP 18 " --> pdb=" O ARGBP 14 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.661A pdb=" N GLYBQ 17 " --> pdb=" O ARGBQ 13 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 removed outlier: 3.576A pdb=" N TYRBR 18 " --> pdb=" O ARGBR 14 " (cutoff:3.500A) Processing helix chain 'BS' and resid 9 through 40 removed outlier: 3.511A pdb=" N GLYBS 17 " --> pdb=" O ARGBS 13 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYRBS 18 " --> pdb=" O ARGBS 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.524A pdb=" N GLYBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYRBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BU' and resid 9 through 40 Processing helix chain 'BV' and resid 9 through 40 removed outlier: 3.561A pdb=" N TYRBV 18 " --> pdb=" O ARGBV 14 " (cutoff:3.500A) Processing helix chain 'BW' and resid 9 through 40 removed outlier: 3.582A pdb=" N TYRBW 18 " --> pdb=" O ARGBW 14 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.792A pdb=" N ARGBX 14 " --> pdb=" O GLUBX 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 195 through 212 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.652A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C1' and resid 127 through 129 No H-bonds generated for 'chain 'C1' and resid 127 through 129' Processing helix chain 'C1' and resid 136 through 142 Processing helix chain 'C1' and resid 161 through 163 No H-bonds generated for 'chain 'C1' and resid 161 through 163' Processing helix chain 'C1' and resid 172 through 175 No H-bonds generated for 'chain 'C1' and resid 172 through 175' Processing helix chain 'C1' and resid 183 through 189 removed outlier: 3.616A pdb=" N ARGC1 189 " --> pdb=" O ALAC1 185 " (cutoff:3.500A) Processing helix chain 'C1' and resid 197 through 199 No H-bonds generated for 'chain 'C1' and resid 197 through 199' Processing helix chain 'C2' and resid 4 through 9 Processing helix chain 'C2' and resid 22 through 52 Processing helix chain 'C2' and resid 55 through 88 removed outlier: 3.985A pdb=" N VALC2 88 " --> pdb=" O ALAC2 84 " (cutoff:3.500A) Processing helix chain 'H1' and resid 7 through 31 removed outlier: 3.702A pdb=" N LYSH1 31 " --> pdb=" O ARGH1 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 22 through 25 No H-bonds generated for 'chain 'H2' and resid 22 through 25' Processing helix chain 'H2' and resid 28 through 30 No H-bonds generated for 'chain 'H2' and resid 28 through 30' Processing helix chain 'H2' and resid 54 through 56 No H-bonds generated for 'chain 'H2' and resid 54 through 56' Processing helix chain 'H2' and resid 115 through 117 No H-bonds generated for 'chain 'H2' and resid 115 through 117' Processing helix chain 'H2' and resid 121 through 124 Processing helix chain 'H2' and resid 140 through 143 Processing helix chain 'H2' and resid 155 through 171 removed outlier: 3.573A pdb=" N GLYH2 168 " --> pdb=" O TYRH2 164 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HISH2 169 " --> pdb=" O TYRH2 165 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N METH2 170 " --> pdb=" O ALAH2 166 " (cutoff:3.500A) Processing helix chain 'H2' and resid 174 through 177 Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 19 through 22 removed outlier: 4.011A pdb=" N PHE L 22 " --> pdb=" O GLY L 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 19 through 22' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 110 Processing helix chain 'L' and resid 116 through 132 removed outlier: 4.062A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.947A pdb=" N TYR L 164 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.732A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.638A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 Processing helix chain 'M' and resid 54 through 79 removed outlier: 3.581A pdb=" N VAL M 79 " --> pdb=" O MET M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 167 removed outlier: 3.575A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) Proline residue: M 164 - end of helix Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.902A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 224 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.549A pdb=" N TRP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.878A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'M' and resid 314 through 319 Processing helix chain 'aa' and resid 3 through 7 Processing helix chain 'aa' and resid 10 through 34 removed outlier: 4.303A pdb=" N VALaa 15 " --> pdb=" O ARGaa 11 " (cutoff:3.500A) Processing helix chain 'aa' and resid 40 through 43 No H-bonds generated for 'chain 'aa' and resid 40 through 43' Processing helix chain 'ab' and resid 3 through 7 Processing helix chain 'ab' and resid 10 through 34 Processing helix chain 'ab' and resid 40 through 43 No H-bonds generated for 'chain 'ab' and resid 40 through 43' Processing helix chain 'ac' and resid 3 through 7 Processing helix chain 'ac' and resid 10 through 33 removed outlier: 3.874A pdb=" N VALac 15 " --> pdb=" O ARGac 11 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALAac 16 " --> pdb=" O ARGac 12 " (cutoff:3.500A) Processing helix chain 'ac' and resid 40 through 43 No H-bonds generated for 'chain 'ac' and resid 40 through 43' Processing helix chain 'ad' and resid 3 through 7 Processing helix chain 'ad' and resid 10 through 34 removed outlier: 3.757A pdb=" N VALad 15 " --> pdb=" O ARGad 11 " (cutoff:3.500A) Processing helix chain 'ad' and resid 40 through 43 No H-bonds generated for 'chain 'ad' and resid 40 through 43' Processing helix chain 'ae' and resid 3 through 7 Processing helix chain 'ae' and resid 10 through 34 removed outlier: 3.835A pdb=" N VALae 15 " --> pdb=" O ARGae 11 " (cutoff:3.500A) Processing helix chain 'ae' and resid 40 through 43 No H-bonds generated for 'chain 'ae' and resid 40 through 43' Processing helix chain 'af' and resid 3 through 7 Processing helix chain 'af' and resid 10 through 34 removed outlier: 3.572A pdb=" N VALaf 15 " --> pdb=" O ARGaf 11 " (cutoff:3.500A) Processing helix chain 'af' and resid 40 through 43 No H-bonds generated for 'chain 'af' and resid 40 through 43' Processing helix chain 'ag' and resid 3 through 7 Processing helix chain 'ag' and resid 10 through 34 removed outlier: 3.616A pdb=" N VALag 15 " --> pdb=" O ARGag 11 " (cutoff:3.500A) Processing helix chain 'ag' and resid 40 through 43 No H-bonds generated for 'chain 'ag' and resid 40 through 43' Processing helix chain 'ah' and resid 3 through 7 Processing helix chain 'ah' and resid 10 through 34 removed outlier: 3.717A pdb=" N VALah 15 " --> pdb=" O ARGah 11 " (cutoff:3.500A) Processing helix chain 'ah' and resid 40 through 43 No H-bonds generated for 'chain 'ah' and resid 40 through 43' Processing helix chain 'ai' and resid 3 through 7 Processing helix chain 'ai' and resid 10 through 34 removed outlier: 4.054A pdb=" N VALai 15 " --> pdb=" O ARGai 11 " (cutoff:3.500A) Processing helix chain 'ai' and resid 40 through 43 No H-bonds generated for 'chain 'ai' and resid 40 through 43' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 34 removed outlier: 4.083A pdb=" N VALaj 15 " --> pdb=" O ARGaj 11 " (cutoff:3.500A) Processing helix chain 'aj' and resid 40 through 43 No H-bonds generated for 'chain 'aj' and resid 40 through 43' Processing helix chain 'ak' and resid 3 through 7 Processing helix chain 'ak' and resid 10 through 33 removed outlier: 4.084A pdb=" N VALak 15 " --> pdb=" O ARGak 11 " (cutoff:3.500A) Processing helix chain 'ak' and resid 40 through 43 No H-bonds generated for 'chain 'ak' and resid 40 through 43' Processing helix chain 'al' and resid 3 through 7 Processing helix chain 'al' and resid 10 through 34 removed outlier: 3.888A pdb=" N VALal 15 " --> pdb=" O ARGal 11 " (cutoff:3.500A) Processing helix chain 'al' and resid 40 through 43 No H-bonds generated for 'chain 'al' and resid 40 through 43' Processing helix chain 'am' and resid 3 through 7 Processing helix chain 'am' and resid 10 through 33 removed outlier: 3.646A pdb=" N VALam 15 " --> pdb=" O ARGam 11 " (cutoff:3.500A) Processing helix chain 'am' and resid 40 through 43 No H-bonds generated for 'chain 'am' and resid 40 through 43' Processing helix chain 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 Processing helix chain 'an' and resid 40 through 43 No H-bonds generated for 'chain 'an' and resid 40 through 43' Processing helix chain 'ao' and resid 3 through 7 Processing helix chain 'ao' and resid 10 through 34 removed outlier: 3.876A pdb=" N VALao 15 " --> pdb=" O ARGao 11 " (cutoff:3.500A) Processing helix chain 'ao' and resid 40 through 43 No H-bonds generated for 'chain 'ao' and resid 40 through 43' Processing helix chain 'ap' and resid 3 through 6 Processing helix chain 'ap' and resid 10 through 34 Processing helix chain 'ap' and resid 40 through 43 No H-bonds generated for 'chain 'ap' and resid 40 through 43' Processing helix chain 'ba' and resid 9 through 40 Processing helix chain 'bb' and resid 9 through 40 removed outlier: 3.508A pdb=" N TYRbb 18 " --> pdb=" O ARGbb 14 " (cutoff:3.500A) Processing helix chain 'bc' and resid 9 through 40 Processing helix chain 'bd' and resid 9 through 40 removed outlier: 3.558A pdb=" N TYRbd 18 " --> pdb=" O ARGbd 14 " (cutoff:3.500A) Processing helix chain 'be' and resid 9 through 40 Processing helix chain 'bf' and resid 9 through 40 removed outlier: 3.574A pdb=" N GLYbf 17 " --> pdb=" O ARGbf 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYRbf 18 " --> pdb=" O ARGbf 14 " (cutoff:3.500A) Processing helix chain 'bg' and resid 9 through 40 removed outlier: 3.580A pdb=" N TYRbg 18 " --> pdb=" O ARGbg 14 " (cutoff:3.500A) Processing helix chain 'bh' and resid 9 through 40 removed outlier: 3.612A pdb=" N TYRbh 18 " --> pdb=" O ARGbh 14 " (cutoff:3.500A) Processing helix chain 'bi' and resid 9 through 40 Processing helix chain 'bj' and resid 9 through 40 removed outlier: 3.538A pdb=" N GLYbj 17 " --> pdb=" O ARGbj 13 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYRbj 18 " --> pdb=" O ARGbj 14 " (cutoff:3.500A) Processing helix chain 'bk' and resid 9 through 40 Processing helix chain 'bl' and resid 9 through 40 removed outlier: 3.515A pdb=" N ARGbl 14 " --> pdb=" O GLUbl 10 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYRbl 18 " --> pdb=" O ARGbl 14 " (cutoff:3.500A) Processing helix chain 'bm' and resid 9 through 40 removed outlier: 3.540A pdb=" N TYRbm 18 " --> pdb=" O ARGbm 14 " (cutoff:3.500A) Processing helix chain 'bn' and resid 9 through 40 removed outlier: 3.691A pdb=" N TYRbn 18 " --> pdb=" O ARGbn 14 " (cutoff:3.500A) Processing helix chain 'bo' and resid 9 through 40 Processing helix chain 'bp' and resid 9 through 40 removed outlier: 3.547A pdb=" N TYRbp 18 " --> pdb=" O ARGbp 14 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 Processing sheet with id= B, first strand: chain 'H2' and resid 5 through 7 Processing sheet with id= C, first strand: chain 'H2' and resid 51 through 53 removed outlier: 6.783A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYRH2 99 " --> pdb=" O LEUH2 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H2' and resid 130 through 132 removed outlier: 3.822A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) 2459 hydrogen bonds defined for protein. 7200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.38 Time building geometry restraints manager: 19.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 13423 1.34 - 1.55: 43723 1.55 - 1.76: 368 1.76 - 1.97: 498 1.97 - 2.18: 448 Bond restraints: 58460 Sorted by residual: bond pdb=" C27 V7Nbc 101 " pdb=" C28 V7Nbc 101 " ideal model delta sigma weight residual 1.348 1.525 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C27 V7NBD 101 " pdb=" C28 V7NBD 101 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C27 V7NBF 101 " pdb=" C28 V7NBF 101 " ideal model delta sigma weight residual 1.348 1.521 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C27 V7Nbi 101 " pdb=" C28 V7Nbi 101 " ideal model delta sigma weight residual 1.348 1.521 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C27 V7NBU1001 " pdb=" C28 V7NBU1001 " ideal model delta sigma weight residual 1.348 1.521 -0.173 2.00e-02 2.50e+03 7.46e+01 ... (remaining 58455 not shown) Histogram of bond angle deviations from ideal: 84.50 - 103.49: 1727 103.49 - 122.47: 69098 122.47 - 141.46: 9260 141.46 - 160.44: 314 160.44 - 179.43: 20 Bond angle restraints: 80419 Sorted by residual: angle pdb=" C34 V7NBJ1001 " pdb=" C9 V7NBJ1001 " pdb=" C8 V7NBJ1001 " ideal model delta sigma weight residual 68.18 123.92 -55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBK1001 " pdb=" C9 V7NBK1001 " pdb=" C8 V7NBK1001 " ideal model delta sigma weight residual 68.18 123.88 -55.70 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBG1001 " pdb=" C9 V7NBG1001 " pdb=" C8 V7NBG1001 " ideal model delta sigma weight residual 68.18 123.77 -55.59 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C34 V7NBW1001 " pdb=" C9 V7NBW1001 " pdb=" C8 V7NBW1001 " ideal model delta sigma weight residual 68.18 123.65 -55.47 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C34 V7NAM1001 " pdb=" C9 V7NAM1001 " pdb=" C8 V7NAM1001 " ideal model delta sigma weight residual 68.18 123.55 -55.37 3.00e+00 1.11e-01 3.41e+02 ... (remaining 80414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 34712 35.71 - 71.41: 1350 71.41 - 107.12: 479 107.12 - 142.82: 123 142.82 - 178.53: 85 Dihedral angle restraints: 36749 sinusoidal: 22304 harmonic: 14445 Sorted by residual: dihedral pdb=" CBD BCLAQ 104 " pdb=" CGD BCLAQ 104 " pdb=" O2D BCLAQ 104 " pdb=" CED BCLAQ 104 " ideal model delta sinusoidal sigma weight residual -180.00 -43.33 -136.67 1 5.00e+00 4.00e-02 6.63e+02 dihedral pdb=" C1 BCLAK 102 " pdb=" C2 BCLAK 102 " pdb=" C3 BCLAK 102 " pdb=" C5 BCLAK 102 " ideal model delta sinusoidal sigma weight residual 180.00 2.45 177.55 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLBP1003 " pdb=" CGA BCLBP1003 " pdb=" O2A BCLBP1003 " pdb=" CBA BCLBP1003 " ideal model delta sinusoidal sigma weight residual -180.00 -137.84 -42.16 1 6.00e+00 2.78e-02 6.90e+01 ... (remaining 36746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 7557 0.122 - 0.244: 641 0.244 - 0.365: 7 0.365 - 0.487: 4 0.487 - 0.609: 3 Chirality restraints: 8212 Sorted by residual: chirality pdb=" C8 BCLBS1004 " pdb=" C10 BCLBS1004 " pdb=" C7 BCLBS1004 " pdb=" C9 BCLBS1004 " both_signs ideal model delta sigma weight residual False 2.70 2.09 0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" C5' LMTBK1004 " pdb=" C4' LMTBK1004 " pdb=" C6' LMTBK1004 " pdb=" O5' LMTBK1004 " both_signs ideal model delta sigma weight residual False -2.51 -1.97 -0.54 2.00e-01 2.50e+01 7.34e+00 chirality pdb=" C8 UYHai 102 " pdb=" C7 UYHai 102 " pdb=" C9 UYHai 102 " pdb=" O7 UYHai 102 " both_signs ideal model delta sigma weight residual False -2.56 -3.05 0.49 2.00e-01 2.50e+01 6.10e+00 ... (remaining 8209 not shown) Planarity restraints: 9122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7NBV1001 " -0.234 2.00e-02 2.50e+03 3.27e-01 1.07e+03 pdb=" C27 V7NBV1001 " 0.509 2.00e-02 2.50e+03 pdb=" C28 V7NBV1001 " -0.334 2.00e-02 2.50e+03 pdb=" C29 V7NBV1001 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbi 101 " 0.153 2.00e-02 2.50e+03 2.95e-01 8.70e+02 pdb=" C27 V7Nbi 101 " -0.393 2.00e-02 2.50e+03 pdb=" C28 V7Nbi 101 " 0.386 2.00e-02 2.50e+03 pdb=" C29 V7Nbi 101 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbd 101 " 0.181 2.00e-02 2.50e+03 1.78e-01 3.18e+02 pdb=" C27 V7Nbd 101 " -0.201 2.00e-02 2.50e+03 pdb=" C28 V7Nbd 101 " -0.154 2.00e-02 2.50e+03 pdb=" C29 V7Nbd 101 " 0.173 2.00e-02 2.50e+03 ... (remaining 9119 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 357 2.59 - 3.17: 43863 3.17 - 3.74: 90044 3.74 - 4.32: 138675 4.32 - 4.90: 221300 Nonbonded interactions: 494239 Sorted by model distance: nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.010 2.260 nonbonded pdb=" CE1 HISAR 29 " pdb="MG BCLAR 101 " model vdw 2.089 3.130 nonbonded pdb=" NE2 HIS C 138 " pdb="FE HEC C1004 " model vdw 2.122 3.080 nonbonded pdb=" O HOHAN 201 " pdb=" O HOHAN 202 " model vdw 2.206 2.440 nonbonded pdb=" O HOHAK 202 " pdb=" O HOHAK 203 " model vdw 2.207 2.440 ... (remaining 494234 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 'AA' and resid 1 through 48) selection = (chain 'AB' and resid 1 through 48) selection = (chain 'AC' and resid 1 through 48) selection = (chain 'AD' and resid 1 through 48) selection = (chain 'AE' and resid 1 through 48) selection = (chain 'AF' and resid 1 through 48) selection = (chain 'AG' and resid 1 through 48) selection = (chain 'AH' and resid 1 through 48) selection = (chain 'AI' and resid 1 through 48) selection = (chain 'AJ' and resid 1 through 48) selection = (chain 'AK' and resid 1 through 48) selection = (chain 'AL' and resid 1 through 48) selection = (chain 'AM' and resid 1 through 48) selection = (chain 'AN' and resid 1 through 48) selection = (chain 'AO' and resid 1 through 48) selection = (chain 'AP' and resid 1 through 48) selection = (chain 'AQ' and resid 1 through 48) selection = (chain 'AR' and resid 1 through 48) selection = (chain 'AS' and resid 1 through 48) selection = (chain 'AT' and resid 1 through 48) selection = (chain 'AU' and resid 1 through 48) selection = (chain 'AV' and resid 1 through 48) selection = (chain 'AW' and resid 1 through 48) selection = (chain 'AX' and resid 1 through 48) } ncs_group { reference = (chain 'BA' and resid 6 through 44) selection = (chain 'BB' and resid 6 through 44) selection = (chain 'BC' and resid 6 through 44) selection = (chain 'BD' and resid 6 through 44) selection = (chain 'BE' and resid 6 through 44) selection = (chain 'BF' and resid 6 through 44) selection = (chain 'BG' and resid 6 through 44) selection = (chain 'BH' and resid 6 through 44) selection = (chain 'BI' and resid 6 through 44) selection = (chain 'BJ' and resid 6 through 44) selection = (chain 'BK' and resid 6 through 44) selection = (chain 'BL' and resid 6 through 44) selection = (chain 'BM' and resid 6 through 44) selection = (chain 'BN' and resid 6 through 44) selection = (chain 'BO' and resid 6 through 44) selection = (chain 'BP' and resid 6 through 44) selection = (chain 'BQ' and resid 6 through 44) selection = (chain 'BR' and resid 6 through 44) selection = (chain 'BS' and resid 6 through 44) selection = (chain 'BT' and resid 6 through 44) selection = (chain 'BU' and resid 6 through 44) selection = (chain 'BV' and resid 6 through 44) selection = (chain 'BW' and resid 6 through 44) selection = (chain 'BX' and resid 6 through 44) selection = (chain 'ba' and resid 6 through 44) selection = (chain 'bb' and resid 6 through 44) selection = (chain 'bc' and resid 6 through 44) selection = (chain 'bd' and resid 6 through 44) selection = (chain 'be' and resid 6 through 44) selection = (chain 'bf' and resid 6 through 44) selection = (chain 'bg' and resid 6 through 44) selection = (chain 'bh' and resid 6 through 44) selection = (chain 'bi' and resid 6 through 44) selection = (chain 'bj' and resid 6 through 44) selection = (chain 'bk' and resid 6 through 44) selection = (chain 'bl' and resid 6 through 44) selection = (chain 'bm' and resid 6 through 44) selection = (chain 'bn' and resid 6 through 44) selection = (chain 'bo' and resid 6 through 44) selection = (chain 'bp' and resid 6 through 44) } ncs_group { reference = chain 'CG' selection = chain 'MG' } ncs_group { reference = (chain 'aa' and resid 2 through 56) selection = (chain 'ab' and resid 2 through 56) selection = (chain 'ac' and resid 2 through 56) selection = (chain 'ad' and resid 2 through 56) selection = (chain 'ae' and resid 2 through 56) selection = (chain 'af' and resid 2 through 56) selection = (chain 'ag' and resid 2 through 56) selection = (chain 'ah' and resid 2 through 56) selection = (chain 'ai' and resid 2 through 56) selection = (chain 'aj' and resid 2 through 56) selection = (chain 'al' and resid 2 through 56) selection = (chain 'am' and resid 2 through 56) selection = (chain 'an' and resid 2 through 56) selection = (chain 'ao' and resid 2 through 56) } ncs_group { reference = chain 'ak' selection = chain 'ap' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.050 Extract box with map and model: 13.850 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 104.170 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.018 0.177 58460 Z= 0.888 Angle : 4.339 55.745 80419 Z= 1.478 Chirality : 0.065 0.609 8212 Planarity : 0.014 0.327 9122 Dihedral : 22.624 178.530 27513 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.38 % Favored : 98.60 % Rotamer: Outliers : 0.28 % Allowed : 2.00 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 4862 helix: 0.85 (0.08), residues: 3234 sheet: -0.53 (0.91), residues: 28 loop : 1.17 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP M 148 HIS 0.013 0.002 HIS M 300 PHE 0.031 0.003 PHEbl 44 TYR 0.047 0.006 TYRao 38 ARG 0.033 0.004 ARGC2 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 810 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 819 average time/residue: 1.7454 time to fit residues: 1741.8395 Evaluate side-chains 592 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 590 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.4457 time to fit residues: 5.2481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AI 37 ASN AR 29 HIS ** AU 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 37 ASN C1 158 GLN C1 199 GLN C2 24 HIS H2 10 ASN H2 12 ASN L 104 GLN L 116 HIS ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN ** ab 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** af 50 GLN ak 36 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 58460 Z= 0.368 Angle : 2.016 31.326 80419 Z= 0.697 Chirality : 0.044 0.361 8212 Planarity : 0.005 0.065 9122 Dihedral : 22.795 179.946 19036 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.30 % Allowed : 9.44 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.12), residues: 4862 helix: 2.53 (0.08), residues: 3235 sheet: 0.30 (1.15), residues: 22 loop : 1.34 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 251 HIS 0.013 0.002 HIS L 153 PHE 0.024 0.002 PHEbe 15 TYR 0.031 0.002 TYR L 164 ARG 0.006 0.001 ARGbh 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 600 time to evaluate : 3.908 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 29 residues processed: 643 average time/residue: 1.7470 time to fit residues: 1381.4916 Evaluate side-chains 596 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 567 time to evaluate : 3.900 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 15 residues processed: 14 average time/residue: 0.6175 time to fit residues: 18.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 448 optimal weight: 0.9980 chunk 369 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 35 GLN AP 11 HIS AR 35 GLN ** AU 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 250 GLN C 251 ASN C1 199 GLN H2 10 ASN H2 12 ASN M 12 GLN aa 50 GLN ab 2 HIS ** ab 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** af 50 GLN ak 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 58460 Z= 0.508 Angle : 1.982 30.375 80419 Z= 0.687 Chirality : 0.048 0.377 8212 Planarity : 0.006 0.073 9122 Dihedral : 22.677 178.863 19036 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.88 % Allowed : 9.99 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.12), residues: 4862 helix: 2.24 (0.08), residues: 3362 sheet: -1.01 (1.63), residues: 12 loop : 1.40 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 148 HIS 0.014 0.002 HIS L 153 PHE 0.025 0.003 PHEBK 15 TYR 0.034 0.002 TYR L 164 ARG 0.008 0.001 ARGAH 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 575 time to evaluate : 3.972 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 49 residues processed: 632 average time/residue: 1.6978 time to fit residues: 1321.6786 Evaluate side-chains 604 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 555 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 33 residues processed: 16 average time/residue: 0.8501 time to fit residues: 24.1608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 0.9990 chunk 311 optimal weight: 0.0170 chunk 215 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 278 optimal weight: 8.9990 chunk 416 optimal weight: 3.9990 chunk 440 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 35 GLN AH 35 GLN ** AN 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AU 37 ASN AW 35 GLN C 71 ASN C1 199 GLN H2 10 ASN ** ab 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ad 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58460 Z= 0.172 Angle : 1.786 31.751 80419 Z= 0.607 Chirality : 0.036 0.328 8212 Planarity : 0.004 0.048 9122 Dihedral : 21.284 179.999 19036 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.20 % Allowed : 11.41 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.12), residues: 4862 helix: 2.86 (0.08), residues: 3368 sheet: -1.28 (1.46), residues: 12 loop : 1.54 (0.18), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 270 HIS 0.009 0.001 HIS L 153 PHE 0.020 0.001 PHEbe 15 TYR 0.018 0.001 TYR L 164 ARG 0.010 0.001 ARGbf 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9724 Ramachandran restraints generated. 4862 Oldfield, 0 Emsley, 4862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 604 time to evaluate : 3.955 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 35 residues processed: 647 average time/residue: 1.6820 time to fit residues: 1350.1619 Evaluate side-chains 585 residues out of total 3995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 550 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 27 residues processed: 8 average time/residue: 0.7479 time to fit residues: 13.6200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7683 > 50: distance: 51 - 72: 8.287 distance: 59 - 83: 6.572 distance: 65 - 94: 24.294 distance: 68 - 72: 5.354 distance: 72 - 73: 6.574 distance: 73 - 74: 20.805 distance: 73 - 76: 29.769 distance: 74 - 75: 18.086 distance: 74 - 83: 25.494 distance: 75 - 108: 40.064 distance: 76 - 77: 26.773 distance: 77 - 78: 20.146 distance: 78 - 79: 19.974 distance: 79 - 80: 11.798 distance: 80 - 81: 11.639 distance: 80 - 82: 21.591 distance: 83 - 84: 4.163 distance: 84 - 85: 17.184 distance: 84 - 87: 16.625 distance: 85 - 86: 18.813 distance: 85 - 94: 13.366 distance: 86 - 120: 22.602 distance: 87 - 88: 29.357 distance: 88 - 89: 36.937 distance: 88 - 90: 35.109 distance: 89 - 91: 30.102 distance: 90 - 92: 28.038 distance: 91 - 93: 23.058 distance: 92 - 93: 15.934 distance: 94 - 95: 33.502 distance: 95 - 96: 35.021 distance: 95 - 98: 15.148 distance: 96 - 97: 16.373 distance: 96 - 104: 13.792 distance: 97 - 128: 6.638 distance: 98 - 99: 31.958 distance: 99 - 100: 51.762 distance: 99 - 101: 37.157 distance: 100 - 102: 30.503 distance: 101 - 103: 9.675 distance: 102 - 103: 11.016 distance: 104 - 105: 21.019 distance: 105 - 106: 24.400 distance: 106 - 107: 27.170 distance: 106 - 108: 5.169 distance: 107 - 135: 22.214 distance: 108 - 109: 11.273 distance: 109 - 110: 32.263 distance: 109 - 112: 24.478 distance: 110 - 111: 3.709 distance: 110 - 120: 9.698 distance: 111 - 142: 38.234 distance: 112 - 113: 10.701 distance: 113 - 114: 23.253 distance: 113 - 115: 8.156 distance: 114 - 116: 16.606 distance: 115 - 117: 16.073 distance: 116 - 118: 30.123 distance: 117 - 118: 18.404 distance: 118 - 119: 15.802 distance: 120 - 121: 10.899 distance: 121 - 122: 33.779 distance: 121 - 124: 3.014 distance: 122 - 123: 40.042 distance: 122 - 128: 22.839 distance: 123 - 146: 23.889 distance: 124 - 125: 33.505 distance: 125 - 126: 17.313 distance: 126 - 127: 30.706 distance: 128 - 129: 29.313 distance: 129 - 130: 21.945 distance: 129 - 132: 23.026 distance: 130 - 131: 20.792 distance: 130 - 135: 12.201 distance: 131 - 153: 27.649 distance: 132 - 133: 27.514 distance: 132 - 134: 21.451 distance: 135 - 136: 17.820 distance: 136 - 137: 16.892 distance: 136 - 139: 5.148 distance: 137 - 138: 27.486 distance: 137 - 142: 30.255 distance: 138 - 160: 20.288 distance: 139 - 140: 10.242 distance: 139 - 141: 18.123 distance: 142 - 143: 12.307 distance: 143 - 144: 20.631 distance: 144 - 145: 12.865 distance: 144 - 146: 26.770 distance: 145 - 164: 12.520 distance: 146 - 147: 21.670 distance: 147 - 148: 3.203 distance: 147 - 150: 16.518 distance: 148 - 149: 17.257 distance: 148 - 153: 11.641 distance: 149 - 170: 20.973 distance: 150 - 151: 32.877 distance: 150 - 152: 37.730